Determination of Hemagglutinin and Neuraminidase Genetic Variation of Human Influenza A(H1N1)pdm09 Virus Strain Isolated From Deceased Patients in Shiraz, Iran: A Cross-Sectional Study.

Background and Aims: A novel strain of influenza A(H1N1) was first detected in April 2009, resulting in a global pandemic. Alterations in its hemagglutinin (HA) and neuraminidase (NA) proteins can impact the virus's properties, pathogenicity, and response to treatment. Thus, ongoing epidemiological and molecular studies are crucial for effective vaccine development and management. We aimed to monitor the evolution of influenza A(H1N1) pdm09 virus (as defined by WHO) in deceased individuals during a specific period in Shiraz, Iran. Methods: A total of 200 post-mortem samples were collected from deceased individuals. Subsequently, the HA and NA gene segments of these viral isolates were subjected to targeted amplification and sequencing. Phylogenetic analysis was then conducted on the HA and NA gene sequences. Results: A total of 21 samples between 2018 and 2019 were confirmed positive for influenza A(H1N1)pdm09 viruses. All strains isolated from deceased patients belonged to subclade 6B.1, with I216T and S162N mutations. Our strains differed from the A/California/07/2009 vaccine strain, with the substitutions S203T, S185T, K163Q, and D222G observed in the HA antigenic epitope. Additionally, E224G, R223Q, and D222G mutations were detected in the RBS of HA. The NA gene analysis of influenza A(H1N1)pdm09 viruses showed sporadic detections of oseltamivir-resistance mutation, H275Y, in 5% of reported sequences. Nevertheless, no other NAI resistance-associated mutations were detected in the NA of these viruses. Conclusion: Our research strains exhibited genetic variations compared to the vaccine strains. The results of this study demonstrate the genetic diversity of influenza A(H1N1)pdm09 viruses and emphasize the critical importance of continued molecular investigations to inform effective influenza control strategies.