Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

Nadeau, Sarah A. and Vaughan, Timothy G. and Beckmann, Christiane and Topolsky, Ivan and Chen, Chaoran and Hodcroft, Emma and Schär, Tobias and Nissen, Ina and Santacroce, Natascha and Burcklen, Elodie and Ferreira, Pedro and Jablonski, Kim Philipp and Posada-Céspedes, Susana and Capece, Vincenzo and Seidel, Sophie and Santamaria de Souza, Noemi and Martinez-Gomez, Julia M. and Cheng, Phil and Bosshard, Philipp P. and Levesque, Mitchell P. and Kufner, Verena and Schmutz, Stefan and Zaheri, Maryam and Huber, Michael and Trkola, Alexandra and Cordey, Samuel and Laubscher, Florian and Gonçalves, Ana Rita and Aeby, Sébastien and Pillonel, Trestan and Jacot, Damien and Bertelli, Claire and Greub, Gilbert and Leuzinger, Karoline and Stange, Madlen and Mari, Alfredo and Roloff, Tim and Seth-Smith, Helena and Hirsch, Hans H. and Egli, Adrian and Redondo, Maurice and Kobel, Olivier and Noppen, Christoph and du Plessis, Louis and Beerenwinkel, Niko and Neher, Richard A. and Beisel, Christian and Stadler, Tanja. (2022) Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Science Translational Medicine, 15 (680). eabn7979.

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Official URL: https://edoc.unibas.ch/91038/

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Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020 - the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland's border closures de-coupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86-98% reduction in introductions during Switzerland's strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred, using a phylodynamic model. We found that transmission slowed 35-63% upon outbreak detection in summer 2020, but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Computational Modeling of Biological Processes (Neher)
UniBasel Contributors:Neher, Richard A
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:American Association for the Advancement of Science
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:21 Feb 2023 10:38
Deposited On:21 Feb 2023 10:38

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