G2c-Lineage Dominance and S1 Epitope-Glycan Drift of Porcine Epidemic Diarrhea Virus in Guangdong Province, China, 2022–2024

Porcine epidemic diarrhea (PED), a severe and highly contagious disease induced by porcine epidemic diarrhea virus (PEDV), impacts pigs across all age groups but has a particularly high lethality in neonatal piglets, with mortality rates reaching 80 to 100%, leading to substantial economic losses in the swine industry. In this investigation, 128 intestinal samples obtained from 65 large-scale pig farms in eight prefectures of Guangdong Province were screened by RT-qPCR between 2022 and 2024. Of these, 50 samples (39.06%) tested positive for Porcine Epidemic Diarrhea Virus (PEDV). The complete S1 genes of 31 representative strains were sequenced. Phylogenetic analysis revealed G2c as the exclusive dominant lineage (29/31, 93.6%), with single representatives of G2a and G2d. Nucleotide identity among the local strains ranged from 88.9 to 100% and 88.1 to 93.5% to prototype CV777 and from 91.2 to 99.1% to vaccine strain AJ1102. The COE neutralizing epitope (aa 499-638) carried 26 substitutions versus AJ1102; T499I/S, A520S/L, F539L, K566N and F615L were most prevalent. The SS2 epitope was fully conserved, whereas SS6 showed three low-frequency changes (S766P, S769F, G770V). Six distinct N-glycosylation patterns were identified relative to AJ1102. The predominance of G2c, accompanied by marked epitope drift and altered glycosylation, indicates the need for further investigation into vaccine efficacy. Continuous surveillance and the careful evaluation of G2c-based vaccine candidates are warranted.