Influenza A and B viruses represent significant global health threats, contributing substantially to morbidity and mortality rates. However, a comprehensive understanding of the molecular epidemiology of these viruses in Brazil, a continental-size country and a crucial hub for the entry, circulation, and dissemination of Influenza viruses within South America, still needs to be improved. This study addresses this gap by consolidating data and samples across all Brazilian macroregions, as part of the Center for Viral Surveillance and Serological Assessment (CeVIVAS) project, together with an extensive number of other Brazilian sequences provided by a public database during the epidemic seasons spanning 2021-2023.

Phylogenetic analysis of the Hemagglutinin segment (HA) of Influenza A/H1N1pdm09, A/H3N2, and Influenza B/Victoria-lineage revealed that in 2021 and in the first semester of 2022 the A/H3N2 2a.3 strain was the predominant circulating strain. Subsequently, the A/H3N2 2b became the prevalent strain until October, when it was substituted by A/H1N1pdm09 5a.2a and 5a.2a.1 lineages. This scenario was maintained during the year of 2023. B/Victoria emerged and circulated at low levels between December 2021 and September 2022, then became co-prevalent with A/H1N1pdm09 5a.2a and 5a.2a.1 lineages.

The comparison between the vaccine strain A/Darwin/9/2021 and circulating viruses revealed shared mutations to aspartic acid at residues 186 and 225 across all A/H3N2 lineages from 2021 to 2023, altering the charge in the RBD domain. For A/H1N1pdm09, the 2022 consensus of 5a.2a.1 and the vaccine strain A/Victoria/2570/2019 showed 14 amino acid substitutions. Key residues H180, D187, K219, R223, E224, and T133 are involved in hydrogen interactions with sialic acids, while N130, K142, and D222 may contribute to distance interactions based on docking analyses.

Importantly, distinct Influenza A lineage frequency patterns were observed across Brazil’s macroregions, underscoring the regional variations in virus circulation. This study characterizes Influenza A and B viruses circulating in Brazil, providing insights into their circulation patterns and dynamics across Brazilian macroregions. These findings hold significant implications for public health interventions, informing strategies to mitigate transmission risks, optimize vaccination efforts, and enhance outbreak control measures.