Molecular epidemiological study of porcine epidemic diarrhea from winter 2020 to spring 2021 in Jiangsu Province

Abstract

Background: Porcine epidemic diarrhea (PED) is an acute and highly contagious infectious disease caused by the porcine epidemic diarrhea virus (PEDV) that occurs most frequently from winter to spring. It is associated with high morbidity and mortality rates, especially among piglets, and causes huge losses in the pig industry. The aim of this molecular epidemiological study was to identify the current strains of PEDV that are prevalent in Jiangsu Province, China.Methods: From winter 2020 to spring 2021, 793 small intestine tissue, fecal, and anal swab samples were collected from 72 pig farms in 11 counties in the jurisdiction of 5 regions of Jiangsu Province (Yancheng, Suqian, Changzhou, Xuzhou, and Yangzhou). A highly variable region of the S gene was amplified and sequenced, and phylogenetic analysis was conducted to compare this sequence with corresponding sequences from reference strains deposited in GenBank. Results: A total of 457 samples from 57 pig farms were positive for PEDV: this implies a positivity rate of 79% (57/72) for pig farms and a sample positivity rate of 57.6% (457/793). The positivity rates were 78% (107/137) in Yancheng, 53% (218/409) in Suqian, 48% (94/195) in Changzhou, 80% (16/20) in Xuzhou, and 88% (14/16) in Yangzhou. Seven representative samples were selected for sequencing, and phylogenetic analysis showed that the seven isolated strains exhibited 88.0%–100% nucleotide identity and 87.3%–99% amino acid identity. Additionally, our isolates exhibited 88.3%–99.7% nucleotide identity and 88%–98.5% amino acid identity with the reference PEDV strains. Phylogenetic tree analysis indicated that there were considerable difference in the sources of the variants.Conclusions: PEDV had a high infection rate among pigs and is possibly the main pathogenic agent of pig diarrhea in Jiangsu province. Importantly, vaccines must be screened for their efficacy against the newly identified variants.