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Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland.
Chen, Chaoran; Nadeau, Sarah Ann; Topolsky, Ivan; Manceau, Marc; Huisman, Jana S; Jablonski, Kim Philipp; Fuhrmann, Lara; Dreifuss, David; Jahn, Katharina; Beckmann, Christiane; Redondo, Maurice; Noppen, Christoph; Risch, Lorenz; Risch, Martin; Wohlwend, Nadia; Kas, Sinem; Bodmer, Thomas; Roloff, Tim; Stange, Madlen; Egli, Adrian; Eckerle, Isabella; Kaiser, Laurent; Denes, Rebecca; Feldkamp, Mirjam; Nissen, Ina; Santacroce, Natascha; Burcklen, Elodie; Aquino, Catharine; de Gouvea, Andreia Cabral; Moccia, Maria Domenica; Grüter, Simon; Sykes, Timothy; Opitz, Lennart; White, Griffin; Neff, Laura; Popovic, Doris; Patrignani, Andrea; Tracy, Jay; Schlapbach, Ralph; Dermitzakis, Emmanouil T; Harshman, Keith; Xenarios, Ioannis; Pegeot, Henri; Cerutti, Lorenzo; Penet, Deborah; Blin, Anthony; Elies, Melyssa; Althaus, Christian L; Beisel, Christian; Beerenwinkel, Niko.
  • Chen C; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
  • Nadeau SA; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
  • Topolsky I; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
  • Manceau M; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
  • Huisman JS; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland; Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland.
  • Jablonski KP; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
  • Fuhrmann L; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
  • Dreifuss D; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
  • Jahn K; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
  • Beckmann C; Viollier AG, Allschwil, Switzerland.
  • Redondo M; Viollier AG, Allschwil, Switzerland.
  • Noppen C; Viollier AG, Allschwil, Switzerland.
  • Risch L; Dr Risch, Labormedizinisches Zentrum, Switzerland.
  • Risch M; Dr Risch, Labormedizinisches Zentrum, Switzerland.
  • Wohlwend N; Dr Risch, Labormedizinisches Zentrum, Switzerland.
  • Kas S; Dr Risch, Labormedizinisches Zentrum, Switzerland.
  • Bodmer T; Dr Risch, Labormedizinisches Zentrum, Switzerland.
  • Roloff T; Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
  • Stange M; Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
  • Egli A; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
  • Eckerle I; Geneva Center for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
  • Kaiser L; Geneva Center for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
  • Denes R; Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
  • Feldkamp M; Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
  • Nissen I; Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
  • Santacroce N; Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
  • Burcklen E; Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
  • Aquino C; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • de Gouvea AC; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Moccia MD; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Grüter S; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Sykes T; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Opitz L; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • White G; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Neff L; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Popovic D; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Patrignani A; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Tracy J; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Schlapbach R; Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland.
  • Dermitzakis ET; Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland.
  • Harshman K; Health 2030 Genome Center, Geneva, Switzerland; Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland.
  • Xenarios I; Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland.
  • Pegeot H; Health 2030 Genome Center, Geneva, Switzerland.
  • Cerutti L; Health 2030 Genome Center, Geneva, Switzerland.
  • Penet D; Health 2030 Genome Center, Geneva, Switzerland.
  • Blin A; Health 2030 Genome Center, Geneva, Switzerland.
  • Elies M; Health 2030 Genome Center, Geneva, Switzerland.
  • Althaus CL; Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
  • Beisel C; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
  • Beerenwinkel N; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
Epidemics ; 37: 100480, 2021 12.
Article in English | MEDLINE | ID: covidwho-1347598
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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ABSTRACT

BACKGROUND:

In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from the UK and later data from other countries, this variant was estimated to have a transmission fitness advantage of around 40-80 % (Volz et al., 2021; Leung et al., 2021; Davies et al., 2021).

AIM:

This study aims to estimate the transmission fitness advantage and the effective reproductive number of B.1.1.7 through time based on data from Switzerland.

METHODS:

We generated whole genome sequences from 11.8 % of all confirmed SARS-CoV-2 cases in Switzerland between 14 December 2020 and 11 March 2021. Based on these data, we determine the daily frequency of the B.1.1.7 variant and quantify the variant's transmission fitness advantage on a national and a regional scale.

RESULTS:

We estimate B.1.1.7 had a transmission fitness advantage of 43-52 % compared to the other variants circulating in Switzerland during the study period. Further, we estimate B.1.1.7 had a reproductive number above 1 from 01 January 2021 until the end of the study period, compared to below 1 for the other variants. Specifically, we estimate the reproductive number for B.1.1.7 was 1.24 [1.07-1.41] from 01 January until 17 January 2021 and 1.18 [1.06-1.30] from 18 January until 01 March 2021 based on the whole genome sequencing data. From 10 March to 16 March 2021, once B.1.1.7 was dominant, we estimate the reproductive number was 1.14 [1.00-1.26] based on all confirmed cases. For reference, Switzerland applied more non-pharmaceutical interventions to combat SARS-CoV-2 on 18 January 2021 and lifted some measures again on 01 March 2021.

CONCLUSION:

The observed increase in B.1.1.7 frequency in Switzerland during the study period is as expected based on observations in the UK. In absolute numbers, B.1.1.7 increased exponentially with an estimated doubling time of around 2-3.5 weeks. To monitor the ongoing spread of B.1.1.7, our plots are available online.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Journal: Epidemics Year: 2021 Document Type: Article Affiliation country: J.epidem.2021.100480

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Journal: Epidemics Year: 2021 Document Type: Article Affiliation country: J.epidem.2021.100480