Immunoinformatic Approach for Identifying Potential Epitope-Vaccine Target against Structural Polyprotein of Chikungunya Virus

Abstract

Background/Aim: Chikungunya virus (CHIKV) continues to be a public health threat in many areas, particularly West Africa, where it is endemic. Herein, it is a big challenge because there are no specific antiviral treatments and limited vaccine accessibility amid recent regulatory challenges and safety concerns for approved vaccine. Given this challenge, this immunoinformatics study aimed to identify potential epitope-based vaccine targets within the structural polyprotein of CHIKV using sequences from Nigerian and Senegalese isolates.

Methodology: Publicly available CHIKV protein sequences were retrieved. The sequences were predicted by use of BepiPred for lineal B-cell epitopes, NetMHCpan-4.1 server, for HLA-A2, -A3, and -B7 supertype-restricted epitopes, and ElliPro tool for conformational B-cell epitopes.

Results: The predicted T-cell and B-cell epitopes are from the most antigenic CHIKV structural polyprotein, with the potential to induce both humoral and cell-mediated immunity. Linear B-cell epitope prediction revealed a broadly antigenic profile across the ~1200-residue polyprotein, with multiple high- (score >1.0) to medium-confidence, (0.5 < score ≤1.0). Retained continuous epitopes (≥5 residues) were predominantly short-to-moderate (5–12 aa), with some extending to 47 aa, and showed high conservation. Strain-specific variations included the unique Nigerian octapeptide KTDGSHDW and the Senegalese nonamer MGQEPNYHE (with minor extension MGQEPNYHEE in Nigeria). In additionally, the repertoire of predicted HLA- A2, A3 and B7 Supertype-restricted T-cell epitopes were identified sharing immunogenic peptide with the predicted lineal B-cell epitopes.

Conclusion: These findings highlight conserved and variant B- and T-cell epitopes in the CHIKV structural polyprotein as promising candidates for multi-epitope vaccine design, offering a cost-effective strategy to enhance humoral immunity against circulating West African variants. The results address diagnostic and therapeutic gaps in CHIKV management and provide a foundation for future experimental validation, including immunogenicity assays and cross-reactivity testing, to support region-tailored prevention in Nigeria, Senegal, and similar endemic regions.