Background: Influenza A and B viruses are the main agent of the seasonal flu outbreaks and their circulation in each area is important to control pandemic caused by this viruses. The aim of the present study was to identify the molecular and seasonal pattern of influenza virus subtypes to investigate circulating influenza A and B viruses in Tehran, Iran.

Methods and results: A cross sectional study was conducted on 108 positive clinical samples in Tehran, Iran between 2023 and 2024. In order to determined mutations and antigenic changes in IAV, and IBV, a conventional PCR and then sequencing was performed on purified PCR products. Among these, 70 (64.81%), and 38 (35.18%) were IAV, and IBV, respectively. Of the 70 influenza A cases, 45 (64.28%) were subtype H3N2 and 25 (35.71%) were subtype H1N1pdm09. Of 38 influenza B cases, while, 20 was unsuitable and was excluded from study, 23 were further characterized as belonging to the B/Yamagata lineage. We detected 13 distinct amino acid substitutions in the HA1 subunit of H1N1, and 8 amino acid substitutions in HA1 among the H3N2 isolates.

Conclusion: The current phylogenetic study and complete sequencing of the HA and NA gene fragments of influenza viruses A and B provide essential information for tracking viral evolution, guiding vaccine development, and ensuring public health preparedness against influenza outbreaks which will play an increasingly important role in global health initiatives.