A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus

Porcine epidemic diarrhea virus (PEDV) is a lethal coronavirus in neonatal piglets characterized by rapid evolution in both genotype and phenotype. However, the underlying genetic mechanism has not been completely elucidated. In this study, we investigated and characterized PEDV field strains circulating in China between 2021 and 2022, which revealed significant genetic divergence. To improve the classification of PEDV, we developed a site-polymorphism-based genotyping system utilizing global PEDV genetic sequences from public databases. While there are currently multiple genotypic classification-based systems for PEDV, our proposed approach could offer more stable classification by considering both genetic characteristics and evolutionary dynamics. Our analysis indicates that the most prevalent PEDV lineages originated from South Korea and China, with G2c: L4 predominating in China and G2c: L10 in the United States. Importantly, discrete phylogenetic analysis revealed potential evolutionary pathways of PEDV, showing that the termini of the S gene are prone to recombination, while adaptive selection is evident in the middle region. Overall, our findings provide a complementary and practical methodology for PEDV classification and offer novel insights into the evolutionary pathway of coronaviruses.