Longitudinal Genotype Replacement, Recombination and Neutralizing Epitope Variations in Porcine Epidemic Diarrhea Virus at a Commercial Pig Farm in Guangxi, China

Porcine epidemic diarrhea virus (PEDV) causes severe enteric disease in piglets. The spike (S) gene is the major target of neutralizing antibodies and a hotspot for genetic variation. In this study, eight PEDV S-gene sequences were obtained from a commercial pig farm in Guangxi, China, between 2021 and 2025. Phylogenetic analysis assigned all sequences to the G2 genotype, with G2c, G2d, and G2b subclusters detected at different time points. Recombination analysis identified sequence-level recombination signatures in the G2c sequences, with G2b-like and G2d-like sequences as parental relatives. Several amino acid substitutions were located within or adjacent to the COE and SS2 neutralizing epitopes, and N-glycosylation site variations were observed among subclusters. Structural predictions suggest that these combined changes may alter surface antigenic properties and confer immune evasion potential, though functional validation using neutralization assays is still required. These findings provide field-derived evidence for PEDV genetic evolution and recombination within a single swine herd, and support rational vaccine-strain evaluation and on-farm biosecurity strategies.