Prediction of immunological T-cell epitopes of hepatitis C virus genotype 5a

Abstract

Background: Hepatitis C virus (HCV) is a public health problem with almost 170 million people estimated to be infected worldwide and is one of the leading cause hepatocellular carcinoma. Currently, there is no vaccine for HCV infection and the current treatment does not clear the infection in all patients. Because of HCV high diversity, protective vaccines will have to overcome significant viral antigenic diversity. The objective of this study was to predict conserved T-cell epitopes of HCV genotype 5a.Methods & Materials: HCV near full-length sequences proteins were analyzed to predict T-cell epitopes that recognize both major histocompatibility complexes (MHC) I and II in HCV genotype 5a using Propred I and Propred, respectively. The Antigenecity of all the predicted epitopes were analysed using VaxiJen v2.0. All antigenic predicted epitopes were analysed for conservation using the IEDB database in comparison with 10 randomly selected sequences from each of the HCV genotypes 1, 2, 3, 4 and 6.Results: A total of 33 and 51 antigenic epitopes that recognize MHC I and MHC II respectively were predicted. The highest number of MHC I binding epitopes were predicted within the NS3 protein (27.2%), followed by E2 (15.2%), and the least binding protein was the NS5A which was not predicted for any antigenic epitopes. The highest numbers of MHC II binding epitopes were predicted within the NS3 protein with 19.6% followed by NS4B (17.6%) and the E2 was the least binder with 1.9%. More than 80% of the predicted epitopes were conserved in genotype 5a sequences. However, in contrast to genotype 5a more than 45% of the predicted epitopes were conserved in other genotypes. The most conserved epitopes in all genotypes were predicted within the NS3 protein while the least conserved epitopes were predicted in the P7 protein. Conclusion:The predicted conserved epitopes analysed in this study will contribute towards the future design of HCV vaccine candidate to avoid variation in genotypes and as such it will be able to induce broad HCV specific immune responses.