Molecular Characterization and Phylogenetic Analysis of a Novel Porcine Epidemic Diarrhea Virus Circulating in Large-scale Pig Farms in Xinjiang, China

Porcine epidemic diarrhea (PED) is a highly contagious disease caused by porcine epidemic diarrhea virus (PEDV), which is characterized by severe diarrhea and vomiting in lactating piglets, resulting in serious economic losses to the pig industry worldwide. Here, a novel variant strain of PEDV (named PEDV/CH/XC/2020) was isolated from the feces of infected piglets, and subjected to genetic variation and recombination analysis based on whole genome sequencing. The results showed that PEDV/CH/XC/2020 belonged to a GIIa subtype variant strain of PEDV, with the genome of 28128 nt in length, which shared only 94% identities with the vaccine strain CV777. Furthermore, multiple amino acid mutations were occurred in the neutralizing antigenic epitopes of COE (499-638 aa) and S1D (636-789 aa) regions of spike protein. It was worth noting that genetic recombination was occurred in the 24010-26546 nt and 27000-27663 nt regions, suggesting that this isolate may arise from genetic recombination with parental strains such as GD-1, CH/ZMDZY and PEDV-CHZ and continuous mutation in epidemic process. In contrast to other mutant strains, the mutation sites 767F, 838L and 1060C of S protein are unique, which might result in the alterations of virulence and immunogenicity of PEDV/CH/XC/2020. These findings of the molecular characteristic of this novel variant strain provided new insights into the genetic variation and diversity and enriched molecular epidemiological date of PED.