Genetic Diversity, Recombination, and Pathogenicity of Porcine Epidemic Diarrhea Virus Strains Circulating in China During 2023–2024

Porcine epidemic diarrhea virus (PEDV) is an enteric alphacoronavirus that causes severe diarrhea and high mortality in neonatal piglets, posing a persistent threat to the global swine industry. Despite extensive vaccination, PEDV continues to circulate in China, underscoring the need for updated molecular epidemiological surveillance. Here, we investigated the prevalence, genetic diversity, and pathogenicity of PEDV strains circulating in China during 2023-2024. A total of 714 clinical samples were collected from diarrheic pigs in seven major swine-producing regions. PEDV RNA was detected in 36.27% of samples, with substantial positivity observed in both anal and nasal swabs. Phylogenetic analysis based on the full-length S gene revealed that circulating strains clustered into multiple subgroups, including GIa, GIIa, GIIb, and GIIc, with GIIc being predominant, indicating pronounced genetic diversity and co-circulation of distinct lineages. Two PEDV strains were isolated from PEDV-positive intestinal tissues and designated PEDV-HeiHo-2024 (GIIb) and PEDV-NJZU-2024 (GIa). Recombination analysis identified PEDV-HeiHo-2024 as a putative recombinant derived from distinct GII lineage strains. Comparative analyses of key neutralizing epitopes and N-linked glycosylation sites in the S protein revealed substantial divergence from classical vaccine strains. Experimental infection of neonatal piglets demonstrated that PEDV-HeiHo-2024 induced severe diarrhea and characteristic intestinal lesions, confirming its high pathogenicity, whereas PEDV-NJZU-2024 showed no apparent pathogenic effects. Collectively, these findings highlight the continued circulation of genetically diverse and pathogenic PEDV strains in China and emphasize the importance of sustained molecular surveillance and vaccine updates.