Detection and phylogenetic analysis of Porcine epidemic diarrhea virus based on the ORF3 gene in pigs in the north of Vietnam

Abstract

To identify further the infectivity, genetic diversity and molecular characteristics of the porcine epidemic diarrhea virus (PEDV). 286 samples of the intestinal tissue of pigs with severe diarrhea were assessed from 5 provinces in the north of Vietnam. The full-length ORF3 gene of 20 representative field strains from 36 farms in 5 provinces was sequenced and analyzed. The prevalence of PEDV was 90.56% and was detected in 259 of 286 samples, with 94.44% (34 of 36) of pig farms harboring the disease. Based on the phylogenetic analysis of the ORF3 genes, our isolates all fell into group G2 (variants) and showed a close relationship to isolates from Chinese (GH1, QH2, and SX1), Korean (DR13 and DR13 attenuated) sources, and these isolates differed genetically from other Chinese (CH and CV777), Korean (DBI865) and French (CV777) strains. Our isolates also 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: BF, with 6-nt insertion, 4-nt difference, 68-nt deletion and 17-aa deletion at position 63-79 compared to the CV777 attenuated strain. Our ORF3 gene analyses showed that the prevalent PEDV isolates were variants and the isolated strains differed genetically from the vaccine strains. These results demonstrated the existence of genetic diversity among geographically distinct PEDV strains and our study has contributed to conducting further researches into PEDV and on an efficacious vaccine design in the future.