A decade of genomic surveillance tracks the disappearance and reintroduction of seasonal influenza virus in Aotearoa New Zealand

Seasonal influenza virus circulation was eliminated in Aotearoa (New Zealand) from 2020 to 2022, following the nation's stringent public health response to the COVID-19 pandemic. Here, we generate nearly 4,000 influenza virus genomes captured over a decade of national surveillance (2013–2022), encompassing influenza A(H3N2) and A(H1N1)pdm09 subtypes and B/Victoria and B/Yamagata lineages. We show that the reintroduction of influenza virus in 2022, was marked by an early and sharp epidemic dominated by the influenza A/H3N2 clade 3C.2a1b.2a.2a.1. Bayesian phylodynamic inference revealed a collapse in influenza virus diversity during border closures, with the diversity of influenza A(H3N2) partially recovering in 2022. Spatial diffusion modelling of the monophyletic A(H3N2) subclade in 2022 revealed strong source-sink dynamics, with the three healthcare regions in the North Island seeding transmission into the South Island. B/Yamagata lineages remained absent from our surveillance post-pandemic, supporting global evidence of its extinction. These findings highlight how prolonged interruption of viral transmission can reshape epidemic dynamics and reduce viral diversity, underscoring the importance of genomic surveillance in understanding and anticipating the evolution and re-emergence of seasonal pathogens.