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Competition between transmission lineages mediated by human mobility shapes seasonal influenza epidemics in the US

Author

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  • Simon P. J. Jong

    (University of Amsterdam)

  • Andrew J. K. Conlan

    (University of Cambridge)

  • Alvin X. Han

    (University of Amsterdam)

  • Colin A. Russell

    (University of Amsterdam)

Abstract

Due to its climatic variability, complex mobility networks and geographic expanse, the United States represents a compelling setting to explore the transmission processes that lead to heterogeneous yearly seasonal influenza epidemics. By analyzing genomic and epidemiological data collected in the US from 2014 to 2023, we show that epidemics consisted of multiple co-circulating transmission lineages that could emerge from all regions and often rapidly expanded. Lineage spread was characterized by strong spatiotemporal hierarchies and lineage size correlated with timing of establishment in the US. Mechanistic epidemic simulations, supported by phylogeographic analyses, suggest that competition between lineages on a network of human mobility consistent with commuting flows drove lineage dynamics. Our results suggest that the processes that disseminate viruses nationwide are highly structured, but variability in the short-term processes that determine the locations, timing, and explosiveness of initial epidemic sparks limits predictability of regional and national epidemics.

Suggested Citation

  • Simon P. J. Jong & Andrew J. K. Conlan & Alvin X. Han & Colin A. Russell, 2025. "Competition between transmission lineages mediated by human mobility shapes seasonal influenza epidemics in the US," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59757-4
    DOI: 10.1038/s41467-025-59757-4
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    References listed on IDEAS

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    1. Amanda C. Perofsky & Chelsea L. Hansen & Roy Burstein & Shanda Boyle & Robin Prentice & Cooper Marshall & David Reinhart & Ben Capodanno & Melissa Truong & Kristen Schwabe-Fry & Kayla Kuchta & Brian P, 2024. "Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Trevor Bedford & Steven Riley & Ian G. Barr & Shobha Broor & Mandeep Chadha & Nancy J. Cox & Rodney S. Daniels & C. Palani Gunasekaran & Aeron C. Hurt & Anne Kelso & Alexander Klimov & Nicola S. Lewis, 2015. "Global circulation patterns of seasonal influenza viruses vary with antigenic drift," Nature, Nature, vol. 523(7559), pages 217-220, July.
    3. repec:plo:pone00:0128070 is not listed on IDEAS
    4. Simon P. J. Jong & Zandra C. Felix Garza & Joseph C. Gibson & Sarah Leeuwen & Robert P. Vries & Geert-Jan Boons & Marliek Hoesel & Karen Haan & Laura E. Groeningen & Katina D. Hulme & Hugo D. G. Willi, 2024. "Determinants of epidemic size and the impacts of lulls in seasonal influenza virus circulation," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    5. Edward K. S. Lam & Dylan H. Morris & Aeron C. Hurt & Ian G. Barr & Colin A. Russell, 2020. "The impact of climate and antigenic evolution on seasonal influenza virus epidemics in Australia," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    6. Simon Cauchemez & Alain-Jacques Valleron & Pierre-Yves Boëlle & Antoine Flahault & Neil M. Ferguson, 2008. "Estimating the impact of school closure on influenza transmission from Sentinel data," Nature, Nature, vol. 452(7188), pages 750-754, April.
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