Epidemiological investigation and molecular characteristics of porcine epidemic diarrhea virus in central China from 2021 to 2022

Abstract Porcine epidemic diarrhea (PED) caused by porcine epidemic diarrhea virus (PEDV) is an intestinal communicable disease. In recent years, the outbreaks of PED have been caused severe economic losses to the swine industry in the central China. In this study, 1664 swabs of piglets with diarrhea and 906 environmental samples were collected from large-scale pig farms in central China from 2021 to 2022, to investigate the presence of PEDV nucleic acid via real-time PCR assay. Results showed that the positive rate of PEDV among swabs and environmental samples was 23.14% and 28.37%, respectively. Phylogenetic analysis based on the entire S gene showed that 13 PEDV strains were clustered into two subgroups, namely GII-a (n = 10) and S-INDEL (n = 3). Further recombinant analysis indicated that three of the strains originated from intra-genogroup recombination. Moreover, we successfully isolated a novel PEDV strain. In addition, the strain was identified via indirect immunofluorescence assay, infection experiment in newborn piglets and whole genome sequencing and named HB2022 strain. Based on the results of nucleotide sequence analysis of each ORFs, it was found that HB2022 strain belonged to GII-a type and had multiple mutation sites. A three-dimensional structural prediction revealed that mutation sites located in the neutralizing epitope COE altered the protein conformation, which may affect the virulence or pathogenicity of PEDV. In conclusion, this study is of great significance for the selection or development of suitable vaccine products and the reduction of economic losses in the pig industry.