Abstract
Influenza A virus (IAV) is present in most swine-producing countries causing production losses and concerns on public health. In Brazil, influenza is endemic in pig herds, and a great genetic diversity has been described in swine IAVs due to multiple introductions of pre-2009 human-seasonal IAVs followed by reassortment events with 2009 pandemic H1N1 (H1N1pdm) virus. Here, we compile 14 years of IAV monitoring data and describe the subtypes and major lineages of H1 and H3 viruses co-circulating in Brazilian pigs. Using multiplex RT-qPCR and sequencing, we identified H1N1pdm as the most frequently detected virus, accounting for 41.3% of the subtyped samples (165/399), followed by H1huN2 (108/399), H3N2 (77/399), and H1N1hu (9/399). The three dominant subtypes were detected co-circulating annually and consistently in seven of the nine states sampled, as well as among pigs at different production phases. Other reassortants were found sporadically and included H1pdmN2 (22/399) and H1huN1pdm (4/399). The high diversity observed indicates that IAVs from distinct lineages are widely disseminated across the country. These findings strongly suggest substantial movement of pigs between regions and states, which may have implications for vaccine design, disease control, and updating of diagnostic tests. Continuous efforts to monitor IAV are crucial to better understand their ecology and to generate relevant data for pandemic preparedness.