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
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Published:2021-03-25
Issue:4
Volume:9
Page:677
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ISSN:2076-2607
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Container-title:Microorganisms
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language:en
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Short-container-title:Microorganisms
Author:
Goncalves Cabecinhas Ana Rita, Roloff Tim, Stange MadlenORCID, Bertelli Claire, Huber MichaelORCID, Ramette AlbanORCID, Chen ChaoranORCID, Nadeau SarahORCID, Gerth Yannick, Yerly Sabine, Opota OnyaORCID, Pillonel TrestanORCID, Schuster Tobias, Metzger Cesar M. J. A., Sieber JonasORCID, Bel Michael, Wohlwend Nadia, Baumann Christian, Koch Michel C., Bittel Pascal, Leuzinger Karoline, Brunner MyrtaORCID, Suter-Riniker Franziska, Berlinger Livia, Søgaard Kirstine K., Beckmann ChristianeORCID, Noppen Christoph, Redondo Maurice, Steffen Ingrid, Seth-Smith Helena M. B., Mari AlfredoORCID, Lienhard Reto, Risch Martin, Nolte OliverORCID, Eckerle Isabella, Martinetti Lucchini Gladys, Hodcroft Emma B.ORCID, Neher Richard A.ORCID, Stadler Tanja, Hirsch Hans H.ORCID, Leib Stephen L.ORCID, Risch LorenzORCID, Kaiser Laurent, Trkola Alexandra, Greub GilbertORCID, Egli AdrianORCID
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.
Subject
Virology,Microbiology (medical),Microbiology
Cited by
35 articles.
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