Disruption of seasonal influenza circulation and evolution during the 2009 H1N1 and COVID-19 pandemics in Southeastern Asia

Zhiyuan Chen, Joseph L.-H. Tsui, Jun Cai, Shuo Su, Cécile Viboud, Louis Plessis, Philippe Lemey (), Moritz U. G. Kraemer () and Hongjie Yu ()
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Zhiyuan Chen: Fudan University
Joseph L.-H. Tsui: University of Oxford
Jun Cai: Fudan University
Shuo Su: Fudan University
Cécile Viboud: National Institutes of Health
Louis Plessis: ETH Zürich
Philippe Lemey: Rega Institute, KU Leuven
Moritz U. G. Kraemer: University of Oxford
Hongjie Yu: Fudan University

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract 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 seasonal influenza migration network within Southeastern Asia remains unclear, including how pandemic-related disruptions altered this network. We leveraged genetic, epidemiological, and airline travel data between 2007-2023 to characterise the dispersal patterns of influenza A/H3N2 and B/Victoria viruses both out of and within Southeastern Asia, including during perturbations by the 2009 A/H1N1 and COVID-19 pandemics. During the COVID-19 pandemic, consistent autumn-winter movement waves from Southeastern Asia to temperate regions were interrupted for both subtype/lineages, however the A/H1N1 pandemic only disrupted A/H3N2 spread. We find a higher persistence of A/H3N2 than B/Victoria circulation in Southeastern Asia and identify distinct pandemic-related disruptions in A/H3N2 antigenic evolution between two pandemics, compared to interpandemic levels; similar patterns are observed in B/Victoria using genetic distance. 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. Our findings provide insights into the heterogeneous impact of two distinct pandemic-related disruptions on influenza circulation, which can help anticipate the effects of future pandemics and potential mitigation strategies on influenza dynamics.

Date: 2025
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DOI: 10.1038/s41467-025-55840-y

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