Epidemics (Dec 2021)
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland
- Chaoran Chen,
- Sarah Ann Nadeau,
- Ivan Topolsky,
- Marc Manceau,
- Jana S. Huisman,
- Kim Philipp Jablonski,
- Lara Fuhrmann,
- David Dreifuss,
- Katharina Jahn,
- Christiane Beckmann,
- Maurice Redondo,
- Christoph Noppen,
- Lorenz Risch,
- Martin Risch,
- Nadia Wohlwend,
- Sinem Kas,
- Thomas Bodmer,
- Tim Roloff,
- Madlen Stange,
- Adrian Egli,
- Isabella Eckerle,
- Laurent Kaiser,
- Rebecca Denes,
- Mirjam Feldkamp,
- Ina Nissen,
- Natascha Santacroce,
- Elodie Burcklen,
- Catharine Aquino,
- Andreia Cabral de Gouvea,
- Maria Domenica Moccia,
- Simon Grüter,
- Timothy Sykes,
- Lennart Opitz,
- Griffin White,
- Laura Neff,
- Doris Popovic,
- Andrea Patrignani,
- Jay Tracy,
- Ralph Schlapbach,
- Emmanouil T. Dermitzakis,
- Keith Harshman,
- Ioannis Xenarios,
- Henri Pegeot,
- Lorenzo Cerutti,
- Deborah Penet,
- Anthony Blin,
- Melyssa Elies,
- Christian L. Althaus,
- Christian Beisel,
- Niko Beerenwinkel,
- Martin Ackermann,
- Tanja Stadler
Affiliations
- Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
- Sarah Ann Nadeau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
- Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
- Marc Manceau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
- Jana S. Huisman
- 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
- Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
- Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
- David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
- Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
- Christiane Beckmann
- Viollier AG, Allschwil, Switzerland
- Maurice Redondo
- Viollier AG, Allschwil, Switzerland
- Christoph Noppen
- Viollier AG, Allschwil, Switzerland
- Lorenz Risch
- Dr Risch, Labormedizinisches Zentrum, Switzerland
- Martin Risch
- Dr Risch, Labormedizinisches Zentrum, Switzerland
- Nadia Wohlwend
- Dr Risch, Labormedizinisches Zentrum, Switzerland
- Sinem Kas
- Dr Risch, Labormedizinisches Zentrum, Switzerland
- Thomas Bodmer
- Dr Risch, Labormedizinisches Zentrum, Switzerland
- Tim Roloff
- 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
- Madlen Stange
- 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
- Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Isabella Eckerle
- 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
- Laurent Kaiser
- 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
- Rebecca Denes
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Mirjam Feldkamp
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Ina Nissen
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Natascha Santacroce
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Elodie Burcklen
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Catharine Aquino
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Andreia Cabral de Gouvea
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Maria Domenica Moccia
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Simon Grüter
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Timothy Sykes
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Lennart Opitz
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Griffin White
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Laura Neff
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Doris Popovic
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Andrea Patrignani
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Jay Tracy
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
- Emmanouil T. Dermitzakis
- Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland
- Keith Harshman
- Health 2030 Genome Center, Geneva, Switzerland; Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
- Ioannis Xenarios
- Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland
- Henri Pegeot
- Health 2030 Genome Center, Geneva, Switzerland
- Lorenzo Cerutti
- Health 2030 Genome Center, Geneva, Switzerland
- Deborah Penet
- Health 2030 Genome Center, Geneva, Switzerland
- Anthony Blin
- Health 2030 Genome Center, Geneva, Switzerland
- Melyssa Elies
- Health 2030 Genome Center, Geneva, Switzerland
- Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
- Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland; Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
- Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland; Corresponding author at: Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
- Journal volume & issue
-
Vol. 37
p. 100480
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.
