Molecular epidemiology of the hemagglutinin gene of prevalent influenza virus A/H1N1/pdm09 among patient in Iran

Abstract

In 2015, the influenza virus A/H1N1/pdm09 strain outbreak became prevalent throughout the different provinces of Iran. There are relatively limited complete genetic sequences available for this virus from Asian countries. Diagnosis and virological surveillance of influenza is essential for detecting novel genetic variants causing epidemic potential. This study describes the genetic properties of HA genome of influenza A/H1N1 pdm09 viruses circulating in Iran during the 2015/2016 season. In order to investigate the genetic pattern of influenza A/H1N1 pdm09, a total of 1758 nasopharyngeal swabs were screened by real-time RT-PCR. Of those, 510 cases were found to be positive for A/H1N1/pdm09 virus. Evolution of the approximately 100 positive specimens with high virus load was conducted via genomic phylogeny. Phylogenetic analysis of the HA genes of the A/H1N1pdm09 viruses revealed the circulation of clade 6B1, characterized by amino acid substitutions S84N, S162N and I216T, where position 162 became glycosylated. The N-glycosylation of HA protein is post or co-translational modification that affect the evolution of influenza viruses. For influenza A(H1N1) pdm09 viruses, we found more mutations in the antigenic sites than in the stem region. The results of this study confirmed the necessity of constant regular antigenic and molecular surveillance of circulating seasonal influenza viruses.

Keywords: Amino acid substitution; Genetic characterization; Influenza virus; Phylogenetic analysis; pdm09 strain.