Full-genome analysis of the pandemic (H1N1) 2009 influenza viruses isolated in Ukraine during 2009-2017 years

Abstract

Purpose: New studies increasingly use an analysis of the entire genome of influenza viruses that can shed new light on the evolution of viruses and the process of selecting vaccine strains. The purpose of our study was to carry out molecular-genetic and phylogenetic analysis of all genes of pandemic A (H1N1) influenza viruses which circulated in Ukraine during 2009-2017 years. Methods & Materials: Samples were analyzed using real-time polymerase chain reaction (RT-PCR). The sequences of influenza viruses from other countries were received from web-site GISAID using BLAST analysis. The influenza A (H1N1) pdm09 sequences are characterized in a neighbor-joining phylogenetic tree with reference strains rooted from the current vaccine strain, A/California/07/2009-like virus. Phylogenetic analysis was performed using MEGA 7. 3D structures were constructed in Chimera 1.11.2rc software. Results: We have analyzed viruses isolated in Ukraine in the period of 2009 - 2017 year. Over the last five years the HA genes have evolved and eight genetic groups have been designated, with A/California/7/2009 representing group 1. The viruses were isolated in Ukraine during 2009-2017 fell into genetic groups 1, 2, 6, 7 and 8. This study demonstrated mutation in all five HA antigenic sites. In the NA genes were observed mutations H275Y and D151X caused resistance to antiviral drugs in different years. NP genes had mutations N377S and V425I, which can influence the immune response. In 2015-2016 in NP genes emerged two mutations A22T and M105I. All isolates including the A/California/07/2009 vaccine strain had the D21G mutation in the M2 protein, which causes resistance to antiviral drugs such as amantadine and rimantadine. NS1 genes had few mutations: E55E, E125D and N205S, which can inhibit human immune response and increase virulence of the virus. In PA was mutation P560S that increases virulence. In addition, we found unique changes in all genes of the polymerase complex (PA, PB1, and PB2). Conclusion: According to the literature review, mutations acquired in each genome segment, in combination lead to increased virulence of the pandemic A (H1N1) pdm09 influenza viruses. Their impact on the increasing of influenza viruses’ virulence was demonstrated in the experiments on mice.