Microorganisms (Mar 2021)
SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing
- Ana Rita Goncalves Cabecinhas,
- Tim Roloff,
- Madlen Stange,
- Claire Bertelli,
- Michael Huber,
- Alban Ramette,
- Chaoran Chen,
- Sarah Nadeau,
- Yannick Gerth,
- Sabine Yerly,
- Onya Opota,
- Trestan Pillonel,
- Tobias Schuster,
- Cesar M. J. A. Metzger,
- Jonas Sieber,
- Michael Bel,
- Nadia Wohlwend,
- Christian Baumann,
- Michel C. Koch,
- Pascal Bittel,
- Karoline Leuzinger,
- Myrta Brunner,
- Franziska Suter-Riniker,
- Livia Berlinger,
- Kirstine K. Søgaard,
- Christiane Beckmann,
- Christoph Noppen,
- Maurice Redondo,
- Ingrid Steffen,
- Helena M. B. Seth-Smith,
- Alfredo Mari,
- Reto Lienhard,
- Martin Risch,
- Oliver Nolte,
- Isabella Eckerle,
- Gladys Martinetti Lucchini,
- Emma B. Hodcroft,
- Richard A. Neher,
- Tanja Stadler,
- Hans H. Hirsch,
- Stephen L. Leib,
- Lorenz Risch,
- Laurent Kaiser,
- Alexandra Trkola,
- Gilbert Greub,
- Adrian Egli
Affiliations
- Ana Rita Goncalves Cabecinhas
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland
- Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
- Madlen Stange
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
- Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
- Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Alban Ramette
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Yannick Gerth
- Center for Laboratory Medicine, 9001 Saint Gall, Switzerland
- Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland
- Onya Opota
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
- Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
- Tobias Schuster
- Federal Office of Public Health FOPH, 3097 Berne, Switzerland
- Cesar M. J. A. Metzger
- Spiez Laboratory, Federal Office for Civil Protection FOCP, 3700 Spiez, Switzerland
- Jonas Sieber
- Spiez Laboratory, Federal Office for Civil Protection FOCP, 3700 Spiez, Switzerland
- Michael Bel
- Federal Office of Public Health FOPH, 3097 Berne, Switzerland
- Nadia Wohlwend
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland
- Christian Baumann
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- Michel C. Koch
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- Pascal Bittel
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- Karoline Leuzinger
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland
- Myrta Brunner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
- Franziska Suter-Riniker
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- Livia Berlinger
- Bioanalytica AG, 6006 Lucerne, Switzerland
- Kirstine K. Søgaard
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
- Christiane Beckmann
- Viollier AG, 4123 Allschwil, Switzerland
- Christoph Noppen
- Viollier AG, 4123 Allschwil, Switzerland
- Maurice Redondo
- Viollier AG, 4123 Allschwil, Switzerland
- Ingrid Steffen
- Rothen AG, 4002 Basel, Switzerland
- Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
- Alfredo Mari
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
- Reto Lienhard
- ADMED Microbiology, 2300 La Chaux-de-Fonds, Switzerland
- Martin Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland
- Oliver Nolte
- Center for Laboratory Medicine, 9001 Saint Gall, Switzerland
- Isabella Eckerle
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland
- Gladys Martinetti Lucchini
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland
- Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
- Richard A. Neher
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland
- Tanja Stadler
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland
- Hans H. Hirsch
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland
- Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- Lorenz Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland
- Laurent Kaiser
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland
- Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
- Adrian Egli
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
- DOI
- https://doi.org/10.3390/microorganisms9040677
- Journal volume & issue
-
Vol. 9,
no. 4
p. 677
Abstract
The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.
Keywords
