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

Benjamin Faucher, Chiara E. Sabbatini, Peter Czuppon, Moritz U. G. Kraemer, Philippe Lemey, Vittoria Colizza, François Blanquart, Pierre-Yves Boëlle and Chiara Poletto ()
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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
Philippe Lemey: KU Leuven
Vittoria Colizza: Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP)
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

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-46345-1

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