Background/Objectives: Influenza A virus undergoes continuous antigenic drift, necessitating annual vaccine reformulation. Saudi Arabia faces unique epidemiological challenges owing to mass gatherings during religious pilgrimages and the dynamic movement of foreign workers. This study aimed to characterize the genetic diversity of hemagglutinin (HA) and neuraminidase (NA) genes of influenza A viruses circulating in Riyadh and to assess their match with vaccine strains during the 2024–2025 period. Methods: Nasopharyngeal samples (n = 363) were collected from patients presenting with influenza-like illness. RT-PCR was used for detection and subtyping. Sequence and phylogenetic analysis of the complete HA and NA gene sequences from A/H1N1pdm09 strains (n = 7) were then performed.
Results: Of the 363 samples, 110 (30.3%) were positive for influenza A; among these, 68 (61.8%) were A/H1N1pdm09, and 42 (38.2%) were H3N2. Phylogenetic analysis revealed that all A/H1N1pdm09 strains belonged to clade 5a.1, distinct from vaccine strains. In comparison with the vaccine strain A/Wisconsin/67/2022, seven amino acid substitutions in the HA gene and eight in the NA gene were recorded in Saudi circulating strains. The significant genetic divergence between circulating A/H1N1pdm09 strains and current vaccine strains indicates potential vaccine mismatch.
Conclusions: The significant genetic divergence between circulating A/H1N1pdm09 strains and current vaccine strains suggests potential vaccine mismatch. Continuous surveillance programs along with vaccination plans are necessary to tackle the changing influenza A virus strains in the special epidemiological context of Saudi Arabia.