Immunogenic Peptide Prediction of Matrix Protein 1 (M1) in H1N1 and H3N2 Strains of Influenza Virus A

Abstract

H1N1 and H3N2 strains of Influenza A viruses belong to one of the best studied viruses; however no effective prevention against influenza has been developed. Current influenza virus vaccines protect mostly against one particular strain thus regular immunization with updated formulations is necessary against the virus. Hence great challenge in the field of influenza virus research is to design universal vaccine. MUSCLE and AVANA tools were used to find out most conserved peptide sequences of M1. Immunoinformatics tools were used for prediction of immunogenic peptides of Matrix Protein 1 (M1) in H1N1 and H3N2 strains of influenza virus A. Putative epitopes for M1 were predicted from conserved peptide sequences of M1. Three tools NetCTL 1.2, BIMAS and Syfpeithi were used to predict the Class I putative epitopes while three tools, ProPred, IEDB-SMM-align and NetMHCII 2.2 were used to predict the Class II putative epitopes. Immunogenic peptides were identified and selected manually by overlapping putative epitopes predicted from online tools individually for both MHC classes. Finally sequences of predicted peptides for both MHC classes were looked for common region which was selected as common immunogenic peptide. Two common immunogenic peptides were found for M1 in H1N1: (i) MEWLKTRPILS (43-53) and (ii) IRHENRMVLASTTAKAM (173-189) while four common immunogenic peptides were found for M1 in H3N2: (i) VKLYRKLKR (97-105), (ii) FHGAKEIALSYSAGALASC (109-127), (iii) LIYNRMGAVTTEVAFGLVCA (130-149) and (iv) VLASTTAKA (180-188). These predicted peptides are promising candidates to be used as target for vaccine design. For establishing immunogenicity of predicted peptides T cell proliferation assay is need to be performed and for that we have optimized the protocol for PBMC proliferation assay (MTT Assay).