Classification Evolution and Epitope Prediction of the Porcine Epidemic Diarrhea Virus (PEDV) Spike Protein in Thailand (2008–2024): Updated Insights for Preventive Strategies

Abstract

Simple Summary Porcine epidemic diarrhea virus (PEDV) continues to cause severe watery diarrhea and devastating piglet production losses worldwide. To map the long-term evolutionary trends of the virus in Thailand, this study evaluated clinical samples collected over a 16-year period (2008–2024) using a comprehensive molecular and bioinformatic pipeline. By analyzing the predicted full-length spike (S) protein structures modeled from nucleotide sequences, we tracked critical mutational shifts and predicted antigenic variation within major neutralizing domains (including COE, SS2, SS6, and 2C10) that may influence antibody recognition. The findings reveal the emergence of unique insertion/deletion (InDel) strains and establish that primitive Thai strains (Cluster 1) likely represent the original structural template of PEDV in the region prior to subsequent divergence into G1 and G2b-related lineages. Ultimately, this framework bridges genomic evolution with structural biology, providing essential data to guide vaccine selection, optimize planned exposure protocols, and update swine biosecurity strategies.