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Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data
Sarah Nadeau; Christiane Beckmann; Ivan Topolsky; Timothy Vaughan; Emma Hodcroft; Tobias Schaer; Ina Nissen; Natascha Santacroce; Elodie Burcklen; Pedro Ferreira; Kim Philipp Jablonski; Susana Posada-Cespedes; Vincenzo Capece; Sophie Seidel; Noemi Santamaria de Souza; Julia M. Martinez-Gomez; Phil Cheng; Philipp Bosshard; Mitchell P. Levesque; Verena Kufner; Stefan Schmutz; Maryam Zaheri; Michael Huber; Alexandra Trkola; Samuel Cordey; Florian Laubscher; Ana Rita Goncalves; Karoline Leuzinger; Madlen Stange; Alfredo Mari; Tim Roloff; Helena Seth-Smith; Hans H. Hirsch; Adrian Egli; Maurice Redondo; Olivier Kobel; Christoph Noppen; Niko Beerenwinkel; Richard A. Neher; Christian Beisel; Tanja Stadler.
Afiliação
  • Sarah Nadeau; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Christiane Beckmann; Viollier AG, Allschwil, Switzerland
  • Ivan Topolsky; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Timothy Vaughan; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Emma Hodcroft; Biozentrum, University of Basel, Basel, Switzerland
  • Tobias Schaer; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Ina Nissen; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Natascha Santacroce; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Elodie Burcklen; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Pedro Ferreira; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Kim Philipp Jablonski; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Susana Posada-Cespedes; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Vincenzo Capece; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Sophie Seidel; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Noemi Santamaria de Souza; Insitute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
  • Julia M. Martinez-Gomez; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
  • Phil Cheng; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
  • Philipp Bosshard; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
  • Mitchell P. Levesque; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
  • Verena Kufner; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
  • Stefan Schmutz; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
  • Maryam Zaheri; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
  • Michael Huber; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
  • Alexandra Trkola; Institute of Medical Virology, University of Zurich, Zurich, Switzerland
  • Samuel Cordey; Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of
  • Florian Laubscher; Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of
  • Ana Rita Goncalves; Swiss National Reference Centre for Influenza, University Hospitals of Geneva, Geneva, Switzerland
  • Karoline Leuzinger; University Hospital Basel, Basel, Switzerland
  • Madlen Stange; University Hospital Basel, Basel, Switzerland
  • Alfredo Mari; University Hospital Basel, Basel, Switzerland
  • Tim Roloff; University Hospital Basel, Basel, Switzerland
  • Helena Seth-Smith; University Hospital Basel, Basel, Switzerland
  • Hans H. Hirsch; University Hospital Basel, Basel, Switzerland
  • Adrian Egli; University Hospital Basel, Basel, Switzerland
  • Maurice Redondo; Viollier AG, Allschwil, Switzerland
  • Olivier Kobel; Viollier AG, Allschwil, Switzerland
  • Christoph Noppen; Viollier AG, Allschwil, Switzerland
  • Niko Beerenwinkel; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Richard A. Neher; Biozentrum, University of Basel, Basel, Switzerland
  • Christian Beisel; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
  • Tanja Stadler; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
Preprint em Inglês | medRxiv | ID: ppmedrxiv-20212621
ABSTRACT
Pathogen genomes provide insights into their evolution and epidemic spread. We sequenced 1,439 SARS-CoV-2 genomes from Switzerland, representing 3-7% of all confirmed cases per week. Using these data, we demonstrate that no one lineage became dominant, pointing against evolution towards general lower virulence. On an epidemiological level, we report no evidence of cryptic transmission before the first confirmed case. We find many early viral introductions from Germany, France, and Italy and many recent introductions from Germany and France. Over the summer, we quantify the number of non-traceable infections stemming from introductions, quantify the effective reproductive number, and estimate the degree of undersampling. Our framework can be applied to quantify evolution and epidemiology in other locations or for other pathogens based on genomic data. One Sentence SummaryWe quantify SARS-CoV-2 spread in Switzerland based on genome sequences from our nation-wide sequencing effort.
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Texto completo: Disponível Coleções: Preprints Base de dados: medRxiv Idioma: Inglês Ano de publicação: 2020 Tipo de documento: Preprint
Texto completo
Adicionar na Minha BVS
Imprimir
XML
Buscar no Google
Texto completo: Disponível Coleções: Preprints Base de dados: medRxiv Idioma: Inglês Ano de publicação: 2020 Tipo de documento: Preprint