Zika viral proteome analysis reveals an epitope cluster within NS3 helicase as a potential vaccine candidate: an in silico study

Zika virus (ZIKV), a mosquito-borne flavivirus, is now an emerging global public health concern. Currently, the pathogenicity, genetic diversity and the consequences of ZIKV infection are little known and a protective vaccine against ZIKV is urgently needed. In this study, we have taken an immunoinformatics approach to predict epitope cluster regions in the whole proteome (3423 amino acids) of ZIKV. We used a range of bioinformatics algorithms to determine epitopes of CD8⁺ cytotoxic T-cells (CTL), CD4⁺ helper T-cells (THL) and B cells. We have predicted an epitope cluster of 23 contiguous amino acids (region 1989–2011, WLEARMLLDNIYLQDGLIASLYR) residing on the NS3 helicase protein in the ZIKV proteome. This epitope cluster contains fourteen CD4⁺ (THL) epitopes and six CD8⁺ (CTL) epitopes. Finally, we have validated the epitopes by analysing their binding efficiency (binding energy within −4.7 to −6.9 kcal/mol) with specific HLA alleles. The epitope cluster is predicted to provide 93.86% population coverage worldwide. Based on our immunoinformatics analysis, we propose the peptide WLEARMLLDNIYLQDGLIASLYR as a new vaccine candidate against Zika virus for further validation.