Molecular Characterization of a Variant Subgroup GII-a Porcine Epidemic Diarrhea Virus Strain in China

Abstract

Background: Since 2010, variant porcine epidemic diarrhea virus (PEDV) has emerged in several provinces of China. The variant strain causes high mortality of newborn piglets, which has resulted in severe economic losses to the pork breeding industry.Results: A variant PEDV strain, SC-YB73, was isolated and identified in China. Pathological observation showed atrophy of villi and edema in the lamina propria. Sequence analysis indicated that six nucleotides were inserted in the E gene, which was first detected in PEDV strains. Furthermore, fifty nucleotide sites were unique in SC-YB73, when compared with another 28 PEDV strains. Phylogenetic analysis based on the complete genome showed that SC-YB73 was clustered in the variant subgroup GII-a, which is widely prevalent in the pig population in China. Recombination analysis suggested that SC-YB73 originated from the recombination of GDS47, TW/Yunlin550/2018, and COL/Cundinamarca/2014.Conclusion: The present study involved the isolation and genetic characterization of a variant PEDV strain. It will provide essential information for the control of PED outbreaks in China.