Sci Transl Med . Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

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Sci Transl Med


. 2022 Nov 8;eabn7979.
doi: 10.1126/scitranslmed.abn7979. Online ahead of print.
Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data


Sarah A Nadeau ^{1 2} , Timothy G Vaughan ^{1 2} , Christiane Beckmann ³ , Ivan Topolsky ^{1 2} , Chaoran Chen ^{1 2} , Emma Hodcroft ^{2 4} , Tobias Schär ¹ , Ina Nissen ¹ , Natascha Santacroce ¹ , Elodie Burcklen ¹ , Pedro Ferreira ^{1 2} , Kim Philipp Jablonski ^{1 2} , Susana Posada-Céspedes ^{1 2} , Vincenzo Capece ¹ , Sophie Seidel ^{1 2} , Noemi Santamaria de Souza ⁵ , Julia M Martinez-Gomez ⁶ , Phil Cheng ⁶ , Philipp P Bosshard ⁶ , Mitchell P Levesque ⁶ , Verena Kufner ⁷ , Stefan Schmutz ⁷ , Maryam Zaheri ⁷ , Michael Huber ⁷ , Alexandra Trkola ⁷ , Samuel Cordey ⁸ , Florian Laubscher ⁸ , Ana Rita Gonçalves ⁹ , Sébastien Aeby ¹⁰ , Trestan Pillonel ¹⁰ , Damien Jacot ¹⁰ , Claire Bertelli ¹⁰ , Gilbert Greub ¹⁰ , Karoline Leuzinger ^{11 12} , Madlen Stange ^{2 12 13} , Alfredo Mari ^{2 12 13} , Tim Roloff ^{2 12 13} , Helena Seth-Smith ^{2 12 13} , Hans H Hirsch ^{11 12} , Adrian Egli ^{12 13} , Maurice Redondo ³ , Olivier Kobel ³ , Christoph Noppen ³ , Louis du Plessis ^{1 2} , Niko Beerenwinkel ^{1 2} , Richard A Neher ^{2 14} , Christian Beisel ¹ , Tanja Stadler ^{1 2}



Affiliations

• PMID: 36346321
• DOI: 10.1126/scitranslmed.abn7979

Abstract

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.