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; Roloff, Tim; , ; , ; , ; Ramette, Alban; , ; , ; , ; , ; , ; , ; , ; , ; , ; , ; , ; Baumann, Christian; Koch, Michel C.; Bittel, Pascal; ... (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. 677. MDPI 10.3390/microorganisms9040677

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Institute of Clinical Chemistry
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Clinical Microbiology
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Virology
04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Social and Preventive Medicine (ISPM)

UniBE Contributor:

Ramette, Alban Nicolas; Baumann, Christian; Koch, Michel Christoph; Bittel, Pascal; Suter, Franziska Marta; Hodcroft, Emma Britt; Leib, Stephen and Risch, Lorenz

Subjects:

600 Technology > 610 Medicine & health
500 Science > 570 Life sciences; biology
300 Social sciences, sociology & anthropology > 360 Social problems & social services

ISSN:

2076-2607

Publisher:

MDPI

Language:

English

Submitter:

Andrea Flükiger-Flückiger

Date Deposited:

08 Apr 2021 12:04

Last Modified:

08 Apr 2021 12:04

Publisher DOI:

10.3390/microorganisms9040677

PubMed ID:

33806013

Uncontrolled Keywords:

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

BORIS DOI:

10.48350/155654

URI:

https://boris.unibe.ch/id/eprint/155654

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