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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 and Roloff, Tim and Stange, Madlen and Bertelli, Claire and Huber, Michael and Ramette, Alban and Chen, Chaoran and Nadeau, Sarah and Gerth, Yannick and Yerly, Sabine and Opota, Onya and Pillonel, Trestan and Schuster, Tobias and Metzger, Cesar M. J. A. and Sieber, Jonas and Bel, Michael and Wohlwend, Nadia and Baumann, Christian and Koch, Michel C. and Bittel, Pascal and Leuzinger, Karoline and Brunner, Myrta and Suter-Riniker, Franziska and Berlinger, Livia and Søgaard, Kirstine K. and Beckmann, Christiane and Noppen, Christoph and Redondo, Maurice and Steffen, Ingrid and Seth-Smith, Helena M. B. and Mari, Alfredo and Lienhard, Reto and Risch, Martin and Nolte, Oliver and Eckerle, Isabella and Martinetti Lucchini, Gladys and Hodcroft, Emma B. and Neher, Richard A. and Stadler, Tanja and Hirsch, Hans H. and Leib, Stephen L. and Risch, Lorenz and Kaiser, Laurent and Trkola, Alexandra and Greub, Gilbert and Egli, Adrian. (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. Microorganisms, 9 (4). p. 9040677.

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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.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Computational Modeling of Biological Processes (Neher)
UniBasel Contributors:Neher, Richard A
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:MDPI
e-ISSN:2076-2607
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
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Last Modified:24 Feb 2022 09:59
Deposited On:24 Feb 2022 09:59

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