Genomic Characterization and Phylogenetic Analysis of HA and NA Genes of Influenza B Virus in Riyadh (2024–2025): Implications for Vaccine Strain Match

Background: Influenza B virus (IBV) undergoes continuous genetic mutations that can affect vaccine effectiveness and immune evasion. Although considerable research on IBV epidemiology exists globally, understanding of its genetic behavior in Saudi Arabia remains limited. This study characterized the molecular epidemiology of IBV in Riyadh, Saudi Arabia, during the 2024–2025 influenza season and evaluated compatibility with the current vaccine strain. Methods: Nasopharyngeal samples (n = 363) were collected from individuals presenting with influenza-like illness at King Khalid University Hospital in Riyadh. Detection and subtyping of IBV were performed using RT-PCR. Complete sequencing of the hemagglutinin (HA) and neuraminidase (NA) genes was conducted on confirmed IBV isolates (n = 7), followed by phylogenetic analysis, amino acid substitution mapping, and glycosylation site prediction. Results: Of the 363 samples analyzed, 68 (18.7%) tested positive for IBV, with the majority occurring in adult females aged 15–64 years. Phylogenetic analysis revealed that all seven IBV isolates belonged to the Victoria lineage under subclade V1A.3a.2, corresponding to the current vaccine strain and strains from the 2022–2023 epidemic season. However, molecular analysis identified two substitutions (D129N and D197E) located in antigenic loop-150 and 190-helix, respectively, in the HA polypeptide that distinguished our strains from vaccine strain B/Austria/1359417/2021. Importantly, the N-glycosylation site at position 169 (NKT), which was present in B/Riyadh/1/2010, has been lost in the IBV strains circulating during 2020–2025. Conclusions: While phylogenetic clade compatibility indicates potential vaccine efficacy, the identified amino acid variations and loss of the glycosylation site underscore the necessity for ongoing molecular surveillance to monitor antigenic changes and evaluate vaccine effectiveness within the Saudi Arabian population.