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

• Published in: Virus research 2019-01, Vol.259, p.38-45
• Main Authors: Mohebbi, Atefeh, Fotouhi, Fatemeh, Jamali, Abbas, Yaghobi, Ramin, Farahmand, Behrokh, Mohebbi, Reza
• Format: Article
• Language: English
• Subjects: Amino Acid Substitution; Animals; Cell Line; Genetic characterization; Genetic Variation; Genotype; Hemagglutinin Glycoproteins, Influenza Virus - chemistry; Hemagglutinin Glycoproteins, Influenza Virus - genetics; Humans; Influenza A Virus, H1N1 Subtype - classification; Influenza A Virus, H1N1 Subtype - genetics; Influenza virus; Influenza, Human - epidemiology; Influenza, Human - virology; Iran - epidemiology; Models, Molecular; Molecular Epidemiology; Multilocus Sequence Typing; pdm09 strain; Phylogenetic analysis; Phylogeny; Prevalence; Protein Conformation; Seasons
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2018.10.001

•This study describes the genetic properties of HA genome of influenza A/H1N1 pdm09 viruses circulating in Iran during the 2015-2016 season.•HA gene of influenza A/H1N1 viruses were amplified by RT-PCR and sequenced. One hundred samples were aligned and submitted in GenBank.•Based on the sequence analysis, the HA molecules at the amino acid level clustered in 6B.1 clade with the reference virus A/Slovenia/2903/2015.•S162N substitution, specific to subclade 6B.1 virus, generated a new potential n-glycosylation motif within the Sa antigenic site.•This S162N substitution have been found in other HA sequences reported from 2015-2016. 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.