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

Autor: Nadeau SA; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Vaughan TG; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Beckmann C; Viollier AG, 4123 Allschwil, Switzerland., Topolsky I; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Chen C; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Hodcroft E; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.; Institute for Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland., Schär T; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland., Nissen I; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland., Santacroce N; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland., Burcklen E; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland., Ferreira P; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Jablonski KP; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Posada-Céspedes S; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Capece V; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland., Seidel S; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Santamaria de Souza N; Department of Biology, ETH Zurich, 8092 Zurich, Switzerland., Martinez-Gomez JM; Department of Dermatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland., Cheng P; Department of Dermatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland., Bosshard PP; Department of Dermatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland., Levesque MP; Department of Dermatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland., Kufner V; Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland., Schmutz S; Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland., Zaheri M; Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland., Huber M; Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland., Trkola A; Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland., Cordey S; Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, 1205 Geneva, Switzerland., Laubscher F; Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, 1205 Geneva, Switzerland., Gonçalves AR; Swiss National Reference Centre for Influenza, University Hospitals of Geneva, 1205 Geneva, Switzerland., Aeby S; Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland., Pillonel T; Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland., Jacot D; Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland., Bertelli C; Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland., Greub G; Institute of Microbiology, University Hospital Centre and University of Lausanne, 1011 Lausanne, Switzerland., Leuzinger K; Division of Clinical Virology, University Hospital Basel, 4051 Basel, Switzerland.; Department of Biomedicine, University of Basel, 4031 Basel, Switzerland., Stange M; 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., Mari A; 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., Roloff T; 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., Seth-Smith H; 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., Hirsch HH; Division of Clinical Virology, University Hospital Basel, 4051 Basel, Switzerland.; Department of Biomedicine, University of Basel, 4031 Basel, Switzerland., Egli A; Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.; Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland., Redondo M; Viollier AG, 4123 Allschwil, Switzerland., Kobel O; Viollier AG, 4123 Allschwil, Switzerland., Noppen C; Viollier AG, 4123 Allschwil, Switzerland., du Plessis L; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Beerenwinkel N; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Neher RA; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.; Biozentrum, University of Basel, 4056 Basel, Switzerland., Beisel C; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland., Stadler T; Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Jazyk: angličtina
Zdroj: Science translational medicine [Sci Transl Med] 2023 Jan 25; Vol. 15 (680), pp. eabn7979. Date of Electronic Publication: 2023 Jan 25.
DOI: 10.1126/scitranslmed.abn7979
Abstrakt: 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.
Databáze: MEDLINE