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

doi:10.3390/microorganisms9040677

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

Microorganisms. 2021 Mar 25;9(4):677. doi: 10.3390/microorganisms9040677.

Authors

Ana Rita Goncalves Cabecinhas^{1

2}, Tim Roloff^{3

4

5}, Madlen Stange^{3

4

5}, Claire Bertelli⁶, Michael Huber⁷, Alban Ramette⁸, Chaoran Chen⁹, Sarah Nadeau⁹, Yannick Gerth¹⁰, Sabine Yerly^{1

2}, Onya Opota⁶, Trestan Pillonel⁶, Tobias Schuster¹¹, Cesar M J A Metzger¹², Jonas Sieber¹², Michael Bel¹¹, Nadia Wohlwend¹³, Christian Baumann⁸, Michel C Koch⁸, Pascal Bittel⁸, Karoline Leuzinger^{14

15}, Myrta Brunner³, Franziska Suter-Riniker⁸, Livia Berlinger¹⁶, Kirstine K Søgaard^{3

4}, Christiane Beckmann¹⁷, Christoph Noppen¹⁷, Maurice Redondo¹⁷, Ingrid Steffen¹⁸, Helena M B Seth-Smith^{3

4

5}, Alfredo Mari^{3

5}, Reto Lienhard^{19

20}, Martin Risch^{13

20}, Oliver Nolte¹⁰, Isabella Eckerle^{1

2}, Gladys Martinetti Lucchini^{20

21}, Emma B Hodcroft²², Richard A Neher^{5

23}, Tanja Stadler^{5

9}, Hans H Hirsch^{14

15

24}, Stephen L Leib⁸, Lorenz Risch^{13

25

26}, Laurent Kaiser^{1

2}, Alexandra Trkola⁷, Gilbert Greub⁶, Adrian Egli^{2

3

20}

Affiliations

¹ Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland.
² Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland.
³ Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland.
⁴ Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland.
⁵ Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland.
⁶ Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland.
⁷ Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
⁸ Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland.
⁹ Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
¹⁰ Center for Laboratory Medicine, 9001 Saint Gall, Switzerland.
¹¹ Federal Office of Public Health FOPH, 3097 Berne, Switzerland.
¹² Spiez Laboratory, Federal Office for Civil Protection FOCP, 3700 Spiez, Switzerland.
¹³ Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland.
¹⁴ Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland.
¹⁵ Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland.
¹⁶ Bioanalytica AG, 6006 Lucerne, Switzerland.
¹⁷ Viollier AG, 4123 Allschwil, Switzerland.
¹⁸ Rothen AG, 4002 Basel, Switzerland.
¹⁹ ADMED Microbiology, 2300 La Chaux-de-Fonds, Switzerland.
²⁰ Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland.
²¹ EOC Microbiological Laboratory, 6500 Bellinzona, Switzerland.
²² Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland.
²³ Biozentrum, University of Basel, 4056 Basel, Switzerland.
²⁴ Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031 Basel, Switzerland.
²⁵ Faculty of Medical Sciences, Private University of the Principality of Liechtenstein, 9495 Triesen, Liechtenstein.
²⁶ Centre of Laboratory Medicine, University Institute of Clinical Chemistry, University of Bern, 3010 Bern, Switzerland.

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: COVID-19; N501Y; SARS-CoV-2; Switzerland; molecular epidemiology; mutation; sequencing; surveillance; variant.