Molecular and antigenic landscape of Influenza viruses circulating in Brazil during the 2025 season

Background: Following the disruptions caused by the COVID-19 pandemic, influenza virus circulation in Brazil has been gradually re-establishing its pre-pandemic seasonality. Sustained genomic and antigenic monitoring by the National Influenza Centres (NICs) plays a pivotal role in characterizing viral evolution, informing vaccine strain selection, and ensuring robust preparedness for potential pandemic scenarios. Methods: The positivity of samples collected under Brazil's Ministry of Health (MoH) National Respiratory Viruses Surveillance Network, sourced from both, Influenza-Like Illness (ILI) sentinel sites and severe acute respiratory infection (SARI) universal surveillance were determined from epidemiological week (EW) 35/2024 to EW 35/2025 using seven-target respiratory virus panel followed by an in-house subtyping protocol. Whole-genome characterization was performed by M-RT-PCR protocol sequencing. Antigenic properties were evaluated by hemagglutination inhibition (HI) assays using ferret antisera provided by the WHO. Antiviral resistance mutations were assessed through NA and PA gene analyses and a phenotypic assay for oseltamivir phosphate (OST) susceptibility. Results: Among 106,740 ILI samples, 12.8% were positive for influenza A or B. Influenza A(H1N1)pdm09 predominated, followed by influenza B/Victoria lineage and A(H3N2) at lower levels. Co-circulation of multiple subclades was observed: A(H1N1)pdm09 (5a.2a.1 D.3.1, D.5), A(H3N2) (J.2.3 replacing J.2 within 2a.3a.1), and B/Victoria (C.5.1, C.5.7). All isolates were antigenically similar to vaccine reference strains. Antiviral resistance analysis identified eight H275Y NA mutations in A(H1N1)pdm09, associated with high reduced inhibition (HRI) to OST along with some NA and PA substitution, indicating potentially HRI or RI to peramivir or baloxavir (BXM), respectively. No B/Yamagata viruses were detected. One zoonotic A(H3N2)v case was reported in Paraná. Conclusions: Influenza activity in Brazil during 2024–2025 reflected global circulation trends, dominated by A(H1N1)pdm09 and B/Victoria lineages with minimal antigenic drift. Continued integrated genomic and antigenic surveillance remains critical to guide vaccine strain selection and detect emerging variants with zoonotic potential or antiviral resistance profile.