Abstract / Summary
Influenza viruses continuously evolve, resulting in genetic diversity that contributes to influenza epidemics and pandemics. This high mutation rate increases the probability of immune evasion, thereby reducing vaccine effectiveness. This study aimed to investigate the genomic and molecular changes in influenza A/H1N1 viruses during 2023–2025. In this study, whole-genome sequencing (WGS) of 30 influenza A(H1N1)pdm09 strains circulating in Iran during the 2023–2024 and 2024–2025 seasons was performed using Oxford Nanopore Technology. Subsequently, genomic, molecular, and phylogenetic analyses were performed, and vaccine efficacy was estimated using the epitope method. Whole-genome sequencing of influenza A/H1N1 viruses revealed that the strains circulating during the 2024–2025 season had a slightly lower similarity to the vaccine strain (98.78%) than those circulating during the 2023–2024 season (99.13%). Epitope A was the most diverse region during both seasons, with estimated vaccine efficacy against the dominant epitope ranging from 38.1% to 50.5% during 2023–2025. Several substitutions were identified in the internal proteins, of which the virulence-associated I123V substitution in NS1 was detected in both the vaccine and analyzed strains. Moreover, the studied strains remained largely susceptible to neuraminidase inhibitors, although one strain carried the S247N substitution. Phylogenetic analysis revealed that 90% of Iranian strains clustered within the 6B.1 A.5a.2a clade, which included globally circulating viruses from the same seasons. Despite topological differences among the phylogenetic trees, no reassortment was detected. The epitope landscape of Iranian A(H1N1)pdm09 viruses circulating during the 2023–2024 and 2024–2025 influenza seasons showed that their genetic makeup underwent seasonal changes due to antigenic drift in HA and NA. Despite these changes, the circulating strains remained closely related to the corresponding vaccine strain, and the estimated vaccine efficacy against the epitopes with the highest number of substitutions was acceptable, consistent with the WHO recommendation to retain A/Wisconsin/67/2022 for the 2025–2026 seasonal vaccine. This study emphasizes the importance of national influenza surveillance within global frameworks to monitor antigenic changes, assess pandemic risks, guide vaccine strain selection, and evaluate antiviral resistance.