INDENTIFYING FUNCTIONALLY CONSERVED REGIONS AND PREDICTING T-CELL EPITOPES ON PROTEINS OF INFLUENZA A VIRUS

Abstract

Influenza A viruses are of worldwide concerns because of their rapidly and endlessly genetic changes. Based on the experimental influenza A virus databases, we analyzed conserved regions on the protein sequences of influenza A virus to facilitate the design of universal vaccine and the prediction of changing tendency of influenza A viral strains. Our study was carried out on eleven viral functional proteins: HA, NA, PA, NS1, NS2, M1, M2, NP, PB1, PB1_F2 and PB2. From these groups, the clusters were formed on subtypes, hosts, countries and years of collection, followed by multiple sequence alignments by two tools ClustalW and MAFFT. Conserved sequences of 9 amino acid residues were selected and used for T-cell epitope prediction by SEP (System for Epitope Prediction). In addition, we also predicted the function of these conserved regions using information on function of influenza A viral proteins from the Swissprot database.