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Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses

Author

Listed:
  • Sama Goliaei

    (Helmholtz Centre for Infection Research
    Technische Universität Braunschweig)

  • Mohammad-Hadi Foroughmand-Araabi

    (Helmholtz Centre for Infection Research
    Technische Universität Braunschweig)

  • Aideen Roddy

    (Helmholtz Centre for Infection Research
    Technische Universität Braunschweig)

  • Ariane Weber

    (Max-Planck Institute of Geoanthropology)

  • Sanni Översti

    (Max-Planck Institute of Geoanthropology)

  • Denise Kühnert

    (Max-Planck Institute of Geoanthropology
    German COVID Omics Initiative (deCOI)
    Robert Koch Institute)

  • Alice C. McHardy

    (Helmholtz Centre for Infection Research
    Technische Universität Braunschweig
    German COVID Omics Initiative (deCOI))

Abstract

During the early stages of the SARS-CoV-2 pandemic, before vaccines were available, nonpharmaceutical interventions (NPIs) such as reducing contacts or antigenic testing were used to control viral spread. Quantifying their success is therefore key for future pandemic preparedness. Using 1.8 million SARS-CoV-2 genomes from systematic surveillance, we study viral lineage importations into Germany for the third pandemic wave from late 2020 to early 2021, using large-scale Bayesian phylogenetic and phylogeographic analysis with a longitudinal assessment of lineage importation dynamics over multiple sampling strategies. All major nationwide NPIs were followed by fewer importations, with the strongest decreases seen for free rapid tests, the strengthening of regulations on mask-wearing in public transport and stores, as well as on internal movements and gatherings. Most SARS-CoV-2 lineages first appeared in the three most populous states with most cases, and spread from there within the country. Importations rose before and peaked shortly after the Christmas holidays. The substantial effects of free rapid tests and obligatory medical/surgical mask-wearing suggests these as key for pandemic preparedness, given their relatively few negative socioeconomic effects. The approach relates environmental factors at the host population level to viral lineage dissemination, facilitating similar analyses of rapidly evolving pathogens in the future.

Suggested Citation

  • Sama Goliaei & Mohammad-Hadi Foroughmand-Araabi & Aideen Roddy & Ariane Weber & Sanni Översti & Denise Kühnert & Alice C. McHardy, 2024. "Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48641-2
    DOI: 10.1038/s41467-024-48641-2
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    References listed on IDEAS

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    1. Mrinank Sharma & Sören Mindermann & Charlie Rogers-Smith & Gavin Leech & Benedict Snodin & Janvi Ahuja & Jonas B. Sandbrink & Joshua Teperowski Monrad & George Altman & Gurpreet Dhaliwal & Lukas Finnv, 2021. "Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    2. Thomas Hale & Noam Angrist & Rafael Goldszmidt & Beatriz Kira & Anna Petherick & Toby Phillips & Samuel Webster & Emily Cameron-Blake & Laura Hallas & Saptarshi Majumdar & Helen Tatlow, 2021. "A global panel database of pandemic policies (Oxford COVID-19 Government Response Tracker)," Nature Human Behaviour, Nature, vol. 5(4), pages 529-538, April.
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