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.
Highlights
Porcine epidemic diarrhea (PED) has increased in severity in China since 2010
porcine epidemic diarrhea virus (PEDV) detection PEDV were detected by PCR on 94.03% (63 of 67) pig farms in 17 cities, and 92.25% (119 of 129) of samples were positive for PEDV in clinical diseased samples
Phylogenetic analysis of the S1 gene According to the phylogenetic analysis of the S1 gene, 21 PEDV isolates in this study (Table 3) were all subtype G2 and were distributed in two subgroups: 2a circulating PEDV and 2b circulating PEDV (Fig. 1a)
Summary
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. The seven ORFs encode four structural proteins, spike (S), envelope (E), membrane (M) and nucleocapsid (N) and three non-structural proteins, replicases 1a, 1b and ORF3 [7, 8]. For non-structural proteins, replicases 1a and 1b are multi-functional and associated with viral genome replication [12], and the accessory ORF3 protein is thought to influence virulence [13]
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