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.

Details

Serval ID
serval:BIB_C7CA145091AD
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
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.
Journal
Microorganisms
Author(s)
Goncalves Cabecinhas A.R., Roloff T., Stange M., Bertelli C., Huber M., Ramette A., Chen C., Nadeau S., Gerth Y., Yerly S., Opota O., Pillonel T., Schuster T., Metzger CMJA, Sieber J., Bel M., Wohlwend N., Baumann C., Koch M.C., Bittel P., Leuzinger K., Brunner M., Suter-Riniker F., Berlinger L., Søgaard K.K., Beckmann C., Noppen C., Redondo M., Steffen I., Seth-Smith HMB, Mari A., Lienhard R., Risch M., Nolte O., Eckerle I., Martinetti Lucchini G., Hodcroft E.B., Neher R.A., Stadler T., Hirsch H.H., Leib S.L., Risch L., Kaiser L., Trkola A., Greub G., Egli A.
ISSN
2076-2607 (Print)
ISSN-L
2076-2607
Publication state
Published
Issued date
25/03/2021
Peer-reviewed
Oui
Volume
9
Number
4
Pages
677
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
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
Pubmed
Web of science
Open Access
Yes
Create date
13/04/2021 14:40
Last modification date
10/09/2021 5:38
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