Dataset Information

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.

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.

SUBMITTER: Goncalves Cabecinhas AR

PROVIDER: S-EPMC8064472 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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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.

Goncalves Cabecinhas Ana Rita AR Roloff Tim T Stange Madlen M Bertelli Claire C Huber Michael M Ramette Alban A Chen Chaoran C Nadeau Sarah S Gerth Yannick Y Yerly Sabine S Opota Onya O Pillonel Trestan T Schuster Tobias T Metzger Cesar M J A CMJA Sieber Jonas J Bel Michael M Wohlwend Nadia N Baumann Christian C Koch Michel C MC Bittel Pascal P Leuzinger Karoline K Brunner Myrta M Suter-Riniker Franziska F Berlinger Livia L Søgaard Kirstine K KK Beckmann Christiane C Noppen Christoph C Redondo Maurice M Steffen Ingrid I Seth-Smith Helena M B HMB Mari Alfredo A Lienhard Reto R Risch Martin M Nolte Oliver O Eckerle Isabella I Martinetti Lucchini Gladys G Hodcroft Emma B EB Neher Richard A RA Stadler Tanja T Hirsch Hans H HH Leib Stephen L SL Risch Lorenz L Kaiser Laurent L Trkola Alexandra A Greub Gilbert G Egli Adrian A

Microorganisms 20210325 4

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 ...[more]

PMID: 33806013

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Dataset Information

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.

Publications

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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