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

Article Article scientifique Article Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data eng 2023-01-25 2023-01-25 author Nadeau Sarah 0000-0003-1008-8918 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. author Vaughan Timothy Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. author Beckmann Christiane 0000-0001-9030-083X Viollier AG, 4123 Allschwil, Switzerland. author Topolsky Ivan 0000-0002-7561-0810 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. 512825 author Chen Chaoran 0000-0002-8763-2937 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. author Hodcroft Emma 0000-0002-0078-2212 SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland. 401862 author Schär Tobias Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland. author Nissen Ina Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland. author Santacroce Natascha Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland. author Burcklen Elodie Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland. author Ferreira Pedro 0000-0003-0559-6125 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. author Jablonski Kim Philipp 0000-0002-4166-4343 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. author Posada-Céspedes Susana 0000-0002-7459-8186 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. author Capece Vincenzo Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland. author Seidel Sophie 0000-0002-4484-9888 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. author Santamaria de Souza Noemi 0000-0001-7134-7480 Department of Biology, ETH Zurich, 8092 Zurich, Switzerland. author Martinez-Gomez Julia M 0000-0002-5684-3707 Department of Dermatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland. author Cheng Phil 0000-0003-2940-006X Department of Dermatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland. 418075 author Bosshard Philipp P 0000-0002-1154-2281 Department of Dermatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland. author Levesque Mitchell P 0000-0001-5902-9420 Department of Dermatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland. author Kufner Verena 0000-0003-4233-5952 Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland. author Schmutz Stefan 0000-0002-1955-7007 Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland. author Zaheri Maryam 0000-0003-2777-835X Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland. 681405 author Huber Michael 0000-0002-0384-0000 Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland. author Trkola Alexandra 0000-0003-1013-876X Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland. author Cordey Samuel 0000-0002-2684-5680 Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, 1205 Geneva, Switzerland. 507357 author Laubscher Florian 0000-0002-8803-981X Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, 1205 Geneva, Switzerland. 748134 author Goncalves Cabecinhas Ana Rita 0000-0002-7893-0158 Swiss National Reference Centre for Influenza, University Hospitals of Geneva, 1205 Geneva, Switzerland. 843761 author Aeby Sébastien 0000-0001-9726-7438 Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland. author Pillonel Trestan 0000-0002-5725-7929 Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland. 765415 author Jacot Damien Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland. 707423 author Bertelli Claire 0000-0003-0550-8981 Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland. author Greub Gilbert 0000-0001-9529-3317 Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland. author Leuzinger Karoline 0000-0002-5654-9356 Division of Clinical Virology, University Hospital Basel, 4051 Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031 Basel, Switzerland. author Stange Madlen 0000-0002-4559-2535 SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland. author Mari Alfredo 0000-0002-3871-088X SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland. author Roloff Tim 0000-0003-3435-4723 SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland. author Seth-Smith Helena SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland. author Hirsch Hans H Division of Clinical Virology, University Hospital Basel, 4051 Basel, Switzerland.,Department of Biomedicine, University of Basel, 4031 Basel, Switzerland. author Regli Adrian 0000-0002-3564-8603 Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland. 646294 author Redondo Maurice Viollier AG, 4123 Allschwil, Switzerland. author Kobel Olivier Viollier AG, 4123 Allschwil, Switzerland. author Noppen Christoph 0000-0001-8953-3417 Viollier AG, 4123 Allschwil, Switzerland. author du Plessis Louis 0000-0003-0352-6289 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. author Beerenwinkel Niko 0000-0002-0573-6119 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. author Neher Richard A 0000-0003-2525-1407 SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Biozentrum, University of Basel, 4056 Basel, Switzerland. author Beisel Christian 0000-0001-5360-2193 Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland. author Stadler Tanja 0000-0001-6431-535X Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. eabn7979 10.1126/scitranslmed.abn7979 36346321 1946-6234 PMC9765449 https://www.science.org/doi/full/10.1126/scitranslmed.abn7979 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 decoupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86 to 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 to 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. Humans SARS-CoV-2 / genetics COVID-19 / genetics Public Health Switzerland / epidemiology Communicable Disease Control Genome, Viral / genetics Phylogeny Dewey 616 56 Département de médecine 221 false 400 Virologie clinique 668 Science translational medicine 15 680 8ad40c40-840b-4c05-a784-7a1fc673f9c8 Article (Published version) Public SANadeau_SCordey_Swiss_public_healt.pdf 626210 application/pdf CC BY-4.0 634e07d88d007b67d7e600bd28ce4ad1a0df97f6acbdba4f43d4e37cf19541d8 openAccess Faculté de médecine / Section de médecine clinique / Département de médecine

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Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data	Science translational medicine			2023	82	58

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Hodcroft, Emma