Evolutionary dynamics and antigenic diversity of porcine epidemic diarrhea virus (PEDV) in China: phylogenetic and recombination analyses based on large-scale S gene sequences.

Porcine epidemic diarrhea virus (PEDV) is a significant pathogen severely threatening the global swine industry. Due to its high variability, traditional vaccines have limited effectiveness in prevention and control. In this study, we conducted a systematic analysis of the molecular characteristics and evolutionary dynamics of 1109 PEDV strains circulating in China, focusing on their S gene sequences. Phylogenetic analysis revealed that Chinese PEDV strains could be classified into two major groups: GI (classic) and GII (variant), which were further divided into six subtypes: GIa, GIb, S-INDEL, GIIa, GIIb, and GIIc. Among them, GIIa accounted for 35.62%, GIIb for 25.70%, and GIIc for 26.06% of the total subtypes. Geographical distribution data showed that Guangdong, Sichuan, and Henan were the provinces with the highest incidences of PEDV. Analysis of amino acid mutations in the S protein suggested that GII strains might sustain transmission under immune pressure via a dual strategy of "sialic acid high affinity + immune escape". Recombination analysis indicated that the D0 structural domain, identified as a recombination hotspot, likely drives PEDV cross-species transmission and immune evasion. Glycosylation pattern analysis further demonstrated that GII strains exhibited unique glycosylation patterns at N62 and N118, potentially related to changes in immunogenicity. This study reports amino acid mutations, recombination events, and glycosylation site variation characteristics of Chinese PEDV strains. These findings provide a crucial foundation for elucidating the evolutionary mechanisms of PEDV, optimizing vaccine design, and formulating region-specific prevention and control strategies.