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

Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Aideen Roddy, Ariane Weber, Sanni Översti, Denise Kühnert and Alice C. McHardy ()
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Sama Goliaei: Helmholtz Centre for Infection Research
Mohammad-Hadi Foroughmand-Araabi: Helmholtz Centre for Infection Research
Aideen Roddy: Helmholtz Centre for Infection Research
Ariane Weber: Max-Planck Institute of Geoanthropology
Sanni Översti: Max-Planck Institute of Geoanthropology
Denise Kühnert: Max-Planck Institute of Geoanthropology
Alice C. McHardy: Helmholtz Centre for Infection Research

Nature Communications, 2024, vol. 15, issue 1, 1-11

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-48641-2

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