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Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data.
Nadeau, Sarah A; Vaughan, Timothy G; Beckmann, Christiane; Topolsky, Ivan; Chen, Chaoran; Hodcroft, Emma; Schär, Tobias; Nissen, Ina; Santacroce, Natascha; Burcklen, Elodie; Ferreira, Pedro; Jablonski, Kim Philipp; Posada-Céspedes, Susana; Capece, Vincenzo; Seidel, Sophie; Santamaria de Souza, Noemi; Martinez-Gomez, Julia M; Cheng, Phil; Bosshard, Philipp P; Levesque, Mitchell P; Kufner, Verena; Schmutz, Stefan; Zaheri, Maryam; Huber, Michael; Trkola, Alexandra; Cordey, Samuel; Laubscher, Florian; Gonçalves, Ana Rita; Aeby, Sébastien; Pillonel, Trestan; Jacot, Damien; Bertelli, Claire; Greub, Gilbert; Leuzinger, Karoline; Stange, Madlen; Mari, Alfredo; Roloff, Tim; Seth-Smith, Helena; Hirsch, Hans H; Egli, Adrian; Redondo, Maurice; Kobel, Olivier; Noppen, Christoph; du Plessis, Louis; Beerenwinkel, Niko; Neher, Richard A; Beisel, Christian; Stadler, Tanja.
  • Nadeau SA; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Vaughan TG; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Beckmann C; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Topolsky I; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Chen C; Viollier AG; 4123, Allschwil, Switzerland.
  • Hodcroft E; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Schär T; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Nissen I; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Santacroce N; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Burcklen E; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Ferreira P; Institute for Social and Preventive Medicine, University of Bern; 3012, Bern, Switzerland.
  • Jablonski KP; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Posada-Céspedes S; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, 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.
  • Santamaria de Souza N; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Martinez-Gomez JM; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Cheng P; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Bosshard PP; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Levesque MP; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Kufner V; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Schmutz S; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Zaheri M; Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.
  • Huber M; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Trkola A; Department of Biology, ETH Zurich; 8092, Zurich, Switzerland.
  • Cordey S; Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland.
  • Laubscher F; Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland.
  • Gonçalves AR; Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland.
  • Aeby S; Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland.
  • Pillonel T; Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland.
  • Jacot D; Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland.
  • Bertelli C; Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland.
  • Greub G; Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland.
  • Leuzinger K; Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland.
  • Stange M; Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine; 1205, Geneva, Switzerland.
  • Mari A; Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine; 1205, Geneva, Switzerland.
  • Roloff T; Swiss National Reference Centre for Influenza, University Hospitals of Geneva; 1205, Geneva, Switzerland.
  • Seth-Smith H; Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland.
  • Hirsch HH; Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland.
  • Egli A; Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland.
  • Redondo M; Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland.
  • Kobel O; Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland.
  • Noppen C; Division of Clinical Virology, University Hospital Basel; 4051, Basel, Switzerland.
  • du Plessis L; Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.
  • Beerenwinkel N; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
  • Neher RA; Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.
  • Beisel C; Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland.
  • Stadler T; SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.
Sci Transl Med ; : eabn7979, 2022 Nov 08.
Article in English | MEDLINE | ID: covidwho-2233623
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.

Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study / Prognostic study Language: English Journal: Sci Transl Med Journal subject: Science / Medicine Year: 2022 Document Type: Article Affiliation country: Scitranslmed.abn7979

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study / Prognostic study Language: English Journal: Sci Transl Med Journal subject: Science / Medicine Year: 2022 Document Type: Article Affiliation country: Scitranslmed.abn7979