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

Abstract

Simple Summary Porcine epidemic diarrhoea virus (PEDV) causes devastating watery diarrhoea in neonatal piglets and results in substantial economic losses to the swine industry. Long-term sow vaccination may exert persistent immune pressure that potentially contributes to viral evolution and inter-lineage homologous recombination. In this five-year longitudinal investigation, eight PEDV field isolates were recovered from a single closed commercial pig farm in Guangxi, China. Phylogenetic and recombination analyses demonstrated obvious temporal genotype turnover within the herd: endemic G2d variants prevailed during 2021–2022, followed by the emergence and predominance of novel recombinant G2c strains after 2023. All G2c isolates arose from natural homologous recombination between indigenous farm G2d strains and externally introduced G2b isolates. Fixed amino acid substitutions located in key neutralizing epitopes, combined with systematic N-glycosylation remodelling, reshaped the surface antigen profiles of PEDV, which suggests potential humoral immune evasion capacity. This long-term field investigation depicts a temporal evolution of farm-resident PEDV and provides field-based evidence to support rational vaccine strain updating and targeted on-farm prevention against porcine epidemic diarrhoea.