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Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha

Author

Listed:
  • Benjamin Faucher

    (Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP))

  • Chiara E. Sabbatini

    (Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP))

  • Peter Czuppon

    (University of Münster)

  • Moritz U. G. Kraemer

    (University of Oxford
    University of Oxford)

  • Philippe Lemey

    (KU Leuven)

  • Vittoria Colizza

    (Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP)
    Georgetown University)

  • François Blanquart

    (PSL Research University)

  • Pierre-Yves Boëlle

    (Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP))

  • Chiara Poletto

    (University of Padova)

Abstract

SARS-CoV-2 variants of concern (VOCs) circulated cryptically before being identified as a threat, delaying interventions. Here we studied the drivers of such silent spread and its epidemic impact to inform future response planning. We focused on Alpha spread out of the UK. We integrated spatio-temporal records of international mobility, local epidemic growth and genomic surveillance into a Bayesian framework to reconstruct the first three months after Alpha emergence. We found that silent circulation lasted from days to months and decreased with the logarithm of sequencing coverage. Social restrictions in some countries likely delayed the establishment of local transmission, mitigating the negative consequences of late detection. Revisiting the initial spread of Alpha supports local mitigation at the destination in case of emerging events.

Suggested Citation

  • Benjamin Faucher & Chiara E. Sabbatini & Peter Czuppon & Moritz U. G. Kraemer & Philippe Lemey & Vittoria Colizza & François Blanquart & Pierre-Yves Boëlle & Chiara Poletto, 2024. "Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46345-1
    DOI: 10.1038/s41467-024-46345-1
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    References listed on IDEAS

    as
    1. Philippe Lemey & Samuel L. Hong & Verity Hill & Guy Baele & Chiara Poletto & Vittoria Colizza & Áine O’Toole & John T. McCrone & Kristian G. Andersen & Michael Worobey & Martha I. Nelson & Andrew Ramb, 2020. "Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    2. Anderson F. Brito & Elizaveta Semenova & Gytis Dudas & Gabriel W. Hassler & Chaney C. Kalinich & Moritz U. G. Kraemer & Joses Ho & Houriiyah Tegally & George Githinji & Charles N. Agoti & Lucy E. Matk, 2022. "Global disparities in SARS-CoV-2 genomic surveillance," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Laura Di Domenico & Giulia Pullano & Chiara E. Sabbatini & Pierre-Yves Boëlle & Vittoria Colizza, 2021. "Modelling safe protocols for reopening schools during the COVID-19 pandemic in France," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    4. Giulia Pullano & Laura Di Domenico & Chiara E. Sabbatini & Eugenio Valdano & Clément Turbelin & Marion Debin & Caroline Guerrisi & Charly Kengne-Kuetche & Cécile Souty & Thomas Hanslik & Thierry Blanc, 2021. "Underdetection of cases of COVID-19 in France threatens epidemic control," Nature, Nature, vol. 590(7844), pages 134-139, February.
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