Phylogenetic and computational proteome analysis of Influenza A virus subtype H5N1

Abstract

The avian influenza is an important infectious disease of birds. Its genome consists of negative sense single stranded segmented RNA which encodes 8 structural proteins (HA, NA, PB1, PB2, PA, M1, M2, NP). The most significant surface proteins of influenza A virus subtype H5N1 are hemagglutinin and neuraminidase for pathogenicity in birds to human. The neighbor-joining method with jukes and cantor algorithm was used for predicting the thirty-six hemagglutinin and thirty-seven neuraminidase nucleotide sequences that were used. The phylogenetic analysis with nucleotide sequences showed proximity between different sources of virus in the same country. It was observed that distribution of almost analogous influenza virus infecting different animals in same country. Therefore, the genome of virus encoded the eight structural proteins, which is important for propagation and infection in the host. We have predicted the sub cellular localization of all proteins in the virus targeting the host. These proteins were located in the plasma membrane and host nucleus interacts with DNA. We have also identified the nine motifs viz. N-glycosylation site, Nmyristoylation site, protein kinase C phosphrylation site, casein kinase 2 phosphorylation site, cAMP and cGMP dependent protein kinase phosphorylation site, amidation, cell attachment sequences (RGD), tyrosine kinase, and prokaryotic membrane lipoprotein lipid attachment site in the proteins. These motifs were involved in regulation, activity and stability of virus. This computational study may be easy to understand the proteome function useful for targeting the antiviral drugs against these motifs.