Classification Evolution and Epitope Prediction of the Porcine Epidemic Diarrhea Virus (PEDV) Spike Protein in
Christopher James Stott1,2, Tanakamol Mahawan1,2, Pablo Piñeyro3
1Akkhararatchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand.
Abstract:
This study analyzed Porcine epidemic diarrhea virus (PEDV) spike protein sequences and structures in Thailand from 2008 to 2024 to provide predicted structural templates that could inform regional vaccine selection and planned exposure frameworks. Using an in-silico approach, the researchers reduced sequence redundancy via CD-HIT (v4.8.1), established evolutionary lineages with BEAST (v1.10.4), and reconstructed protein structures using SWISS-MODEL. Structural comparisons and clustering were performed using DALI Z-scores and DBSCAN (v1.2.2), while Discotope 3 (v3.0) and ElliPro mapped B-cell epitope landscapes against a G1 reference strain. The results revealed a major lineage shift from G2a to G2b strains around 2017, with the spike proteins categorized into 14 subtypes and 6 eigenvalue clusters. Notably, minor amino acid substitutions altered properties such as hydrophobicity without disrupting the core structure, and certain deletions caused minimal structural deviations, indicating that sequence data or predicted structures alone do not fully dictate viral virulence or immunogenicity. Furthermore, primitive TH2 strains shared evolutionary links with G1 or US-InDel strains despite their G2 classification, identifying Cluster 1 as a potential ancestral structural type. In conclusion, this updated analysis provides crucial baseline data to optimize regional PEDV preventative measures, though further rigorous structural investigations are needed to definitively link specific spike alterations to virulence and host immune response.
