Disruption of seasonal influenza circulation and evolution during two pandemic events in Southeastern Asia: contrasting the role of human movement and pathogen competition

East, South, and Southeast Asia (together referred to as Southeastern Asia hereafter) have been recognized as critical areas fuelling the global circulation of seasonal influenza. However, the internal migration network of seasonal influenza within Southeastern Asia remains unclear, including how pandemic-related disruptions altered the network structure and circulation dynamics in this region. Here, we leveraged genetic, epidemiological, and airline travel data between 2007-2023 to characterise the multiyear dispersal patterns of influenza A/H3N2 and B/Victoria viruses both out of and within Southeastern Asia, including during seasons marked by perturbations such as the 2009 A/H1N1 and COVID-19 pandemics. We show consistent Autumn-Winter movement waves of A/H3N2 and B/Victoria from Southeastern Asia to temperate regions during interpandemic seasons. During the COVID-19 pandemic this trend was interrupted for both subtypes, however the A/H1N1 pandemic only disrupted A/H3N2 spread. For influenza strains circulating in Southeastern Asia, we find a higher persistence of A/H3N2 than B/Victoria. We find pandemic-related disruptions in A/H3N2 antigenic evolution, with a greater time-advanced antigenic evolution during the 2009 A/H1N1 pandemic, and a greater time-lagged pattern during the COVID-19 pandemic, compared to inter-pandemic levels. Internally, in comparison to the interpandemic seasons, the inferred dispersal rates within Southeastern Asia decreased by 54.7% and 79.2% during the 2009 A/H1N1 and COVID-19 pandemic seasons, respectively; further, the internal movement structure within Southeastern Asia markedly diverged during the COVID-19 pandemic season, and to a lesser extent, during the 2009 A/H1N1 pandemic season. Analyses of the trunk location and phylogenetic similarity further reveal a temporally varying pattern within Southeastern Asia, suggesting a complex source-sink network, with a notable decrease in the mixing of lineages around the COVID-19 pandemic season. Our findings provide insights into the heterogeneous interplay between influenza circulation in Southeastern Asia and two distinct pandemic-related disruptions (strong decline in human movements during the COVID-19 pandemic, pronounced pathogen interference during the A/H1N1 pandemic), which can help anticipate the effects of potential mitigation strategies and the emergence of future influenza pandemic strains on influenza dynamics.