Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland

Epidemics

Lennart Opitz¹  Maria Domenica Moccia¹  Laura Neff¹  Timothy Sykes²  Andreia Cabral de Gouvea²  Maurice Redondo³  Emmanouil T. Dermitzakis⁴  Andrea Patrignani⁵  Ralph Schlapbach⁶  Kim Philipp Jablonski⁷  David Dreifuss⁷  Thomas Bodmer⁷  Lorenz Risch⁷  Sarah Ann Nadeau⁷  Madlen Stange⁷  Christiane Beckmann⁷  Marc Manceau⁷  Nadia Wohlwend⁷  Griffin White⁸  Katharina Jahn⁹  Tim Roloff⁹  Martin Risch⁹  Chaoran Chen⁹  Lara Fuhrmann⁹  Christoph Noppen⁹  Ivan Topolsky⁹  Jana S. Huisman⁹  Sinem Kas⁹  Mirjam Feldkamp^1,10  Elodie Burcklen^1,10  Rebecca Denes^1,10  Ina Nissen^1,10  Natascha Santacroce^1,10  Tanja Stadler^1,11  Melyssa Elies^1,11  Christian L. Althaus^1,11  Christian Beisel^1,11  Niko Beerenwinkel^1,11  Martin Ackermann^1,11  Anthony Blin^1,11  Jay Tracy^1,12  Doris Popovic^1,12  Deborah Penet^1,13  Henri Pegeot^1,13  Lorenzo Cerutti^1,13  Ioannis Xenarios^1,13  Keith Harshman^1,13  Simon Grüter^1,14  Catharine Aquino^1,14  Laurent Kaiser^1,15  Isabella Eckerle^1,15  Adrian Egli^1,15 

[1] Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland;Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland;Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland;Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland;Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland;Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland;Swiss Institute of Bioinformatics, Switzerland;Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland;Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland;Dr Risch, Labormedizinisches Zentrum, Switzerland;Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland;Geneva Center for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland;Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland;Swiss Institute of Bioinformatics, Switzerland;Viollier AG, Allschwil, Switzerland;

关键词: Pandemic;    SARS-CoV-2;    COVID-19;    B.1.1.7;    Transmission advantage;   

DOI  :  

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown