Phylogenetic Divergence and Molecular Signatures of Porcine Epidemic Diarrhea Virus S‐INDEL Subtype

Abstract

Porcine epidemic diarrhea virus (PEDV) continues to evolve under the selective pressures of vaccine‐induced immunity and environmental factors, leading to immune evasion and sustained piglet mortality. In this study, we characterized PEDV field strains collected across China from 2023 to 2026 and observed substantial genetic divergence. Among them, three strains were identified as the S‐INDEL subtype, with each located on a distinct branch of the S‐INDEL phylogenetic tree. Further analysis revealed branch‐specific molecular features. Notably, strains on the S‐INDEL‐CH‐1 and S‐INDEL‐CH‐2 branches carry a three‐nucleotide deletion at positions 416–418 in the S gene. To facilitate rapid discrimination of subtypes within the GI genotype and S‐INDEL subtype, we established a hierarchical typing scheme that combines predicted N‐linked glycosylation site polymorphisms (N1193 and N230) with the S‐INDEL‐specific deletion pattern, enabling rapid preliminary discrimination among PEDV GI genotype (GIa and GIb) and S‐INDEL subtype directly from S gene sequences. Collectively, our findings provide a complementary and practical framework for PEDV GI genotype and S‐INDEL subtype classification and yield new insights into the molecular characteristics of the S‐INDEL subtype.