Peptides containing multiple CD4+ AND CD8+ T CELL epitopes of H5N1 AND H3N2 influenza virus nucleoprotein

Abstract

Subtypes of influenza virus, H5N1 and H3N2 are the causative of ‘avian flu’ and ‘swine flu’ in humans respectively. No single vaccine has been discovered till now, which can protect the world against the ever mutating strain of these influenza A viruses. Considering this fact, conserved regions from nucleoprotein of both the subtypes of influenza virus A isolated from human hosts were identified (≥90% conservation) by computational tool. Epitopes binding to MHC class I and II were predicted from the conserved regions of nucleoprotein by using three different epitope prediction tools for each MHC class I and II. Predicted epitopes were screened for the presence of any similarity with human self proteins. For H5N1, 44 MHC class I and 41 MHC class II epitopes were identified but in case of H3N2, 31 MHC class I and 34 MHC class II epitopes were predicted. Overlapping epitopes were merged to generate putative immunogenic peptide containing both CD8+ and CD4+ T cell predicted epitopes. Population coverage analysis of these epitopes have indicated that they have the capacity to induce a potent immune response among the individuals belonging to different ethnicities around the world. Molecular docking study has shown that eleven nonamers (each for MHC class I and II) common among H5N1, H3N2 and H1N1 have comparative binding energy with naturally bound peptides. All the predicted immunogenic fragments can be considered as the potent candidates for vaccine design against different subtypes of influenza virus.