About: Detection and phylogenetic analysis of porcine epidemic diarrhea virus in central China based on the ORF3 gene and the S1 gene

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About: Detection and phylogenetic analysis of porcine epidemic diarrhea virus in central China based on the ORF3 gene and the S1 gene 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
has title	Detection and phylogenetic analysis of porcine epidemic diarrhea virus in central China based on the ORF3 gene and the S1 gene
Creator	Liu, Chang Wang, Guoqiang Zhang, Gaiping Ji, Pengchao Deng, Ruiguang Su, Yunfang Chen, Yumei Jiang, Dawei Li, Dongliang Liu, Yunchao Song, Yapeng Xing, Guangxu Zhao, Baolei
Source	Medline; PMC
abstract	BACKGROUND: Porcine epidemic diarrhea (PED) has increased in severity in China since 2010. To investigate further the infectivity, genetic diversity and molecular epidemiology of its causative agent, the porcine epidemic diarrhea virus (PEDV), we assessed 129 clinical samples, which were the intestinal tissue of piglets with severe diarrhea, from 17 cities in central China. Both the spike (S) glycoprotein (S1, 1–789 amino acids (aa)) and the full-length ORF3 gene of 21 representative field strains from 21 farms in 11 cities were sequenced and analysed. METHODS: PEDV was detected by reverse transcription-polymerase chain reaction (RT-PCR), and S1 and ORF3 sequences were processed by the Clustal W method via DNAMAN 8 software, and phylogenetic trees were constructed by the neighbor-joining method using MEGA 6 software. RESULTS: The prevalence of PEDV was 92.25% and was detected in 119 of 129 samples, with 94.03% (63 of 67) of pig farms harbouring the disease. According to the phylogenetic analysis of the S1 genes, our isolates all fell into group G2 (variants) and showed a close relationship to isolates from Chinese (HN1303, CH/ZMDZY/11 and AJ1102), Korean (AD01), American (MN, IA1, IA2 and 13–019349) sources, and these isolates differed genetically from other Chinese (LZC, CH/HNZZ/2011 and SD-M) and Korean (SM98) strains as well Japanese (83-P5 and MK) strains. In addition, our isolates differed from attenuated vaccine strains, CV777 (used in China) and DR13 (used in Korea). According to our derived amino acid sequence analysis, we detected one novel variant PEDV, viz: CH/HNLY, with 4-aa insertion/deletion (RSSS/T) at position 375 and 1-aa (D) deletion at position 430 compared to the CV777 attenuated strain. These mutations were located on the receptor binding domain. Our ORF3 gene analyses showed that the prevalent PEDV isolates were variants, and the isolated strains differed genetically from the vaccine strains. CONCLUSIONS: These findings illustrated the existence of genetic diversity among geographically distinct PEDV strains, and our study has provided an impetus to conduct further research on the PEDV receptor binding protein and on the new and efficacious vaccines design. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-016-0646-8) contains supplementary material, which is available to authorized users.
has issue date	2016-11-25(xsd:dateTime)
bibo:doi	10.1186/s12985-016-0646-8
bibo:pmid	27887624
has license	cc-by
sha1sum (hex)	1ef187d95b5c98c9ef187f3b5cf23e276bf1b018
schema:url	https://doi.org/10.1186/s12985-016-0646-8
resource representing a document's title	Detection and phylogenetic analysis of porcine epidemic diarrhea virus in central China based on the ORF3 gene and the S1 gene
has PubMed Central identifier	PMC5123408
has PubMed identifier	27887624
schema:publication	Virol J
resource representing a document's body	covid:1ef187d95b5c98c9ef187f3b5cf23e276bf1b018#body_text
is schema:about of	named entity 'isolated' named entity 'representative' named entity 'disease' named entity 'binding domain' named entity 'receptor' named entity 'cities' named entity 'phylogenetic' named entity 'sequences' named entity 'China' named entity 'epidemic' named entity 'neighbor-joining method' named entity 'CHINA' named entity '129' named entity 'PCR' named entity 'GENETIC DIVERSITY' named entity 'PORCINE EPIDEMIC DIARRHEA' named entity 'RECEPTOR BINDING' named entity 'ITS' named entity 'ATTENUATED' named entity 'STUDY' named entity 'CLUSTAL' named entity 'AMINO ACID SEQUENCE ANALYSIS' named entity 'RESEARCH' named entity 'ORF3' named entity 'CHINESE' named entity 'CAUSATIVE AGENT' named entity 'GENE ANALYSES' named entity 'ISOLATES' named entity '375' named entity 'OUR' named entity 'GENE' named entity 'GROUP' named entity 'NOVEL' named entity 'VARIANT' named entity 'ADDITION' named entity 'PROTEIN ' named entity 'ATTENUATED VACCINE' named entity 'IA2' named entity 'THESE' named entity 'USING' named entity 'CLINICAL' named entity 'PORCINE EPIDEMIC DIARRHEA VIRUS' named entity 'POLYMERASE CHAIN REACTION' named entity 'POSITION' named entity 'REPRESENTATIVE' named entity 'TREES' named entity 'VACCINES' named entity 'DISTINCT' named entity 'DR13' named entity 'AMINO ACIDS' named entity 'KOREAN' named entity '430' named entity 'GENES' named entity 'LENGTH' named entity 'KOREA' named entity 'DISEASE' named entity 'REVERSE TRANSCRIPTION' named entity 'GLYCOPROTEIN' named entity 'PREVALENCE' named entity 'TO INVESTIGATE' named entity 'SEVERITY' named entity 'VACCINE' named entity 'CONCLUSIONS' named entity 'TISSUE' named entity 'SAMPLES' named entity 'METHOD' named entity 'PROCESSED' named entity 'PORCINE EPIDEMIC DIARRHEA VIRUS' named entity 'S1 GENE'

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