Phylogenetic and structural analysis of major surface proteins hemagglutinin and neuraminidase of novel avian influenza virus A H7N9 from chinese patient

Abstract

This research reveals the phylogenetic history and structural information of the hemagglutinin(HA) and neuraminidase(NA) from novel avian influenza virus A/Hangzhou/1/2013(H7N9_2013) strain from human infected in China. Strains closely related to the H7N9_2013 strain were obtained from Nation Center for Biotechnology Information(USA)-basic local alignment search tool(NCBI-BLAST) searching, and the phylogenetic trees were constructed. The 3D structures of HA and NA from H7N9_2013 strain were built by homology modeling technology, and molecular dynamics(MD) simulations were performed on the high-performance computer cluster. Characteristic amino acid sites were then screened from multiple sequence alignment(MSA) via home-made Python script and mapped onto the 3D structures. The thermodynamic characteristic root-mean-square-fluctuation (RMSF) of these sites in the structure was also analyzed with MD trajectories. The HA of H7N9_2013 strain is closely related to the A/duck/Zhejiang/12/2011 strain isolated in China, while the NA of H7N9_2013 strain is mostly related to the A/mallard/Czech Republic/13438-29K/2010 strain isolated in Europe. The 3D structures of HA and NA from H7N9_2013 stain are mostly identical to the existing structure of H7 and N9. A total of 11 and 14 characteristic amino acid sites were identified in HA and NA, respectively, in H7N9_2013. Structural analysis indicates that certain sites in the top region of HA are important, at which the mutation of some amino acids can impact the receptor binding that may be related to its infection of human beings.