IMMUNOINFORMATIC APPROACH FOR IDENTIFYING POTENTIAL EPITOPEVACCINE 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.