Discovery of Targetable Epitopes in Tomato Chlorosis Virus Through Comparative Genomics and Structural Modeling

Tomato chlorosis virus (ToCV) is a highly infectious plant virus that poses a significant threat to the Solanaceae family worldwide. Despite its widespread impact, effective control remains challenging due to its vector-borne transmission by whiteflies. To facilitate early detection and potential therapeutic intervention, this study aimed to identify diagnostic epitopes through a comprehensive bioinformatics approach combining comparative genomics and artificial intelligence-based structural modeling. We analyzed forty-four complete ToCV genomes to identify highly conserved regions and uncovered an orphan clade, indicating evolutionary divergence. Subcellular localization and transmembrane domain predictions revealed viral proteins with extracellularly exposed peptide regions. Structural modeling using AlphaFold3 further validated the stability and accessibility of these domains. By integrating these findings with epitope prediction algorithms, this study identified four highly promising epitope candidates, which are suitable for the development of antibody-based diagnostic kits and antiviral therapeutics targeting ToCV. These epitopes provide a strong foundation for the development of antibody-based diagnostic kits or antiviral therapeutics targeting ToCV.