Post-Pandemic Genomic Diversity and Lineage Turnover of Influenza Viruses in Mexico During 2022-2023

Seasonal influenza circulation was profoundly disrupted during the COVID-19 pandemic, resulting in an unprecedented global decline in viral activity and genetic diversity. As non-pharmaceutical interventions gradually relaxed, influenza viruses re-emerged in multiple regions in 2022; however, genomic data from Latin America remain limited, particularly for the first post-pandemic season. In this study, we analyzed the epidemiological, genomic, and evolutionary patterns of influenza A and B viruses circulating in Mexico between June 2018 and June 2023, with a specific focus on the first post-pandemic season (June 2022-June 2023). More than 90% of the influenza virus genomes available from Mexico for this post-pandemic period were generated in this study, while data from earlier seasons were used for contextualization. Following a near-complete absence of influenza circulation during 2020-2021, viral activity re-emerged in late 2021 and intensified during 2022-2023. Post-pandemic circulation in Mexico was dominated by influenza A(H3N2), with a lower contribution from A(H1N1)pdm09 and a delayed re-emergence of B/Victoria; B/Yamagata was not detected. Genomic analyses revealed rapid lineage turnover after the pandemic, characterized by the predominance of post-pandemic clades and reduced genetic diversity compared with pre-pandemic seasons. Phylogenetic analyses indicated multiple introductions and strong regional connectivity across North and South America.