Whole-Genome Sequencing Tracks Influenza H1N1 Drift in Iran and Backs Current Vaccine Strain

Influenza A(H1N1)pdm09 remains one of the most closely watched respiratory viruses on the planet, and for good reason. Its error-prone RNA polymerase introduces mutations with every replication cycle, allowing the virus to gradually reshape the very surfaces that human antibodies recognize. A new whole-genome sequencing study from Iran, published in Virology Journal, has now provided one of the most detailed national pictures yet of how this virus evolved across two consecutive influenza seasons, from 2023 to 2025, and what that evolution means for vaccine performance. The work, led by researchers at Tehran University of Medical Sciences in collaboration with the Iran National Influenza Center, sequenced thirty complete viral genomes collected during the 2023–2024 and 2024–2025 seasons, using Oxford Nanopore Technology to read all eight genomic segments of each isolate.

The choice of platform matters. Whole-genome sequencing with nanopore devices allows laboratories to generate complete viral genomes rapidly and at relatively low cost, which is essential for surveillance programs that need to keep pace with a virus that evolves on a timescale of months. Rather than focusing solely on the hemagglutinin gene, the conventional workhorse of influenza phylogenetics, the Iranian team examined the entire genome, including the internal proteins that govern replication efficiency, host immune modulation, and antiviral susceptibility. This comprehensive approach is increasingly recognized as essential because changes outside the surface glycoproteins can influence viral fitness and virulence in ways that hemagglutinin-focused studies miss entirely.

The central finding concerns genetic distance from the vaccine strain. Viruses circulating during the 2024–2025 season showed slightly lower nucleotide similarity to the vaccine component, at 98.78 percent, than those from the 2023–2024 season, which stood at 99.13 percent. While a difference of roughly a third of a percentage point may appear trivial, in influenza virology such incremental drift is precisely what accumulates into antigenic change over successive seasons. The result confirms that the Iranian viral population was not static between the two seasons but continued to diverge slowly from the A/Wisconsin/67/2022 vaccine strain, mirroring the global pattern of antigenic drift that the World Health Organization monitors when it convenes its twice-yearly vaccine composition meetings.

To translate raw sequence divergence into immunological terms, the researchers turned their attention to the epitope landscape of the hemagglutinin protein. Epitopes are the discrete regions of viral surface proteins that antibodies actually bind, and mutations concentrated within these regions are far more consequential for immune escape than changes elsewhere in the protein. The analysis revealed that epitope A, one of the five major antigenic sites on the globular head of hemagglutinin, was the most variable region during both seasons. This is consistent with decades of influenza research showing that epitope A sits at the immunodominant tip of the molecule, where antibody pressure is strongest and where substitutions are most readily tolerated structurally.

Using a computational method that estimates vaccine efficacy from the density of substitutions within epitope regions, the team calculated that vaccine protection against the dominant epitope ranged from 38.1 percent to 50.5 percent across the 2023–2025 period. These figures, while moderate, fall within the range typically observed for inactivated influenza vaccines in well-matched seasons, where real-world effectiveness against laboratory-confirmed infection often hovers between 40 and 60 percent. The authors interpret these estimates as acceptable and consistent with the WHO decision to retain A/Wisconsin/67/2022 as the H1N1 component of the 2025–2026 seasonal vaccine. In other words, despite measurable drift, the circulating Iranian viruses had not yet escaped the reach of vaccine-induced immunity.

Beyond the surface glycoproteins, the study documented several substitutions in the internal proteins of the viral genome, a dimension of influenza evolution that receives far less attention in routine surveillance. Among these, the I123V substitution in the non-structural protein NS1 was detected in both the vaccine strain and the analyzed Iranian isolates. NS1 is a multifunctional virulence factor that antagonizes the host interferon response, and substitutions in this protein can modulate how effectively the virus suppresses innate immunity. The presence of the same substitution in both vaccine and circulating strains suggests it is a shared, likely stable feature of the clade rather than a marker of emerging virulence specific to the Iranian isolates.

Antiviral susceptibility is the other critical surveillance question, and here the news was largely reassuring. Neuraminidase inhibitors such as oseltamivir remain the mainstay of influenza antiviral therapy, and resistance mutations in the neuraminidase gene can rapidly undermine treatment, as occurred historically with seasonal H1N1 strains that acquired the H275Y substitution. The Iranian viruses remained largely susceptible to neuraminidase inhibitors throughout the study period, although one strain carried the S247N substitution, a change that has been associated with reduced inhibition in some influenza A viruses and therefore warrants continued monitoring. A single resistant-adjacent variant among thirty genomes does not signal a treatment crisis, but it illustrates exactly the kind of signal that whole-genome surveillance is designed to catch early.

Phylogenetic analysis placed 90 percent of the Iranian strains within clade 6B.1 A.5a.2a, the same subclade that dominated globally during the 2023–2025 seasons. This clustering demonstrates that Iran’s H1N1 population was fully integrated into the worldwide viral lineage structure, with no evidence of a locally divergent or geographically isolated evolutionary trajectory. The researchers also compared the topologies of phylogenetic trees built from different genomic segments, a standard approach for detecting reassortment, the process by which co-infecting viruses exchange entire segments and can generate strains with novel combinations of surface and internal genes. Despite minor topological differences among the trees, no reassortment was detected, indicating that the Iranian viruses evolved through gradual point mutation rather than segment exchange.

The broader significance of the study lies less in any single mutation than in the demonstration of what sustained national sequencing capacity can deliver. Iran sits at a crossroads of human migration and viral traffic, and genomic data from the region fill an important gap in the global influenza surveillance network, which has historically been concentrated in North America, Europe, and East Asia. By showing that circulating strains remained closely matched to the vaccine, that epitope-level drift was measurable but not yet consequential, and that antiviral susceptibility was preserved, the study provides exactly the kind of evidence that informs vaccine strain selection committees and public health planners. The authors emphasize that continued national surveillance within global frameworks is essential for monitoring antigenic change, assessing pandemic risk, guiding vaccine updates, and detecting antiviral resistance before it becomes widespread.

For the coming seasons, the message is one of cautious continuity rather than alarm. The H1N1 viruses circulating in Iran between 2023 and 2025 drifted measurably, concentrated their changes in the most immunologically visible regions of hemagglutinin, and edged slightly further from the vaccine strain with each season, yet they remained recognizably the same clade 6B.1 A.5a.2a viruses that the current vaccine was designed to counter. The estimated epitope-based vaccine efficacy of roughly 38 to 50 percent suggests meaningful, if imperfect, protection, in line with expectations for a well-matched seasonal vaccine. As sequencing technology becomes cheaper and faster, studies of this kind are likely to become the norm rather than the exception, offering public health authorities a near-real-time view of viral evolution and a firmer scientific footing for the annual decisions that determine how well the world’s influenza vaccines match the viruses they must fight.

Subject of Research: Molecular evolution and epitope variation of influenza A(H1N1)pdm09 viruses in Iran based on whole-genome sequencing, 2023–2025

Article Title: Molecular evolution and epitope landscape of influenza A(H1N1) viruses in Iran: insights from whole-genome sequencing (2023–2025)

Article References: Ghadirali, M., Sadeghi, K., Nejati, A., Shabani, M., Zadheidar, S., Ahmadi, A. S., Abedi, A., Yavarian, J., Shafiei-Jandaghi, N. Z., & Mokhtari-Azad, T. (2026). Molecular evolution and epitope landscape of influenza A(H1N1) viruses in Iran: insights from whole-genome sequencing (2023–2025). Virology Journal. https://doi.org/10.1186/s12985-026-03331-x

Image Credits: AI Generated

DOI: 10.1186/s12985-026-03331-x

Keywords: influenza A(H1N1)pdm09, whole-genome sequencing, Oxford Nanopore Technology, antigenic drift, epitope landscape, vaccine efficacy, phylogenetic analysis, clade 6B.1 A.5a.2a, neuraminidase inhibitors, NS1 protein, influenza surveillance, Iran