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

Abstract

BackgroundPorcine 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.MethodsPEDV 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.ResultsThe 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.ConclusionsThese 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 materialThe online version of this article (doi:10.1186/s12985-016-0646-8) contains supplementary material, which is available to authorized users.

Porcine epidemic diarrhea virus ORF3 protein causes endoplasmic reticulum stress to facilitate autophagy

“…The ORF3 protein exhibits a genetic variation among PEDVs. Sequence comparison of virulent and attenuated PEDV strains revealed that some of attenuation-related mutations are located in the ORF3 genes (Chen et al, 2010;Su et al, 2016), suggesting that ORF3 protein exhibits a genetic variation among PEDVs. In addition, ORF3, as the only accessory gene in PEDV, is thought to function as an ion channel and to influence virus production and virulence (Wang et al, 2012).…”

Genome-wide analysis of differentially expressed genes and the modulation of PEDV infection in Vero E6 cells

“…The S protein is the major envelope glycoprotein responsible for receptor binding, virus attachment, cell membrane fusion and entry [7]. M protein, the most abundant surface protein, is co-expressed with E protein to form pseudo-particles which results in interfering genic activity [8]. N protein is highly conserved and the epitopes may be important for induction of cell-mediated immunity [9].…”

Isolation and recombinant analysis of variants of porcine epidemic diarrhea virus strains from Beijing, China

“…Other isolates in 2016 in the Beijing area showed a closer relationship with previous isolates in Guangdong. This revealed that S genes accumulated variations faster based on inherent genetic characteristics or recombinant genes from other isolates [ 10 , 20 , 24 ].…”