Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020-Reference-Cited by-同舟云学术

Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020

Published:2021-01-21 Issue:3 Volume:26 Page:
ISSN:1560-7917
Container-title:Eurosurveillance
language:en
Short-container-title:

Author:

Bal Antonin¹²³,Destras Gregory¹²³,Gaymard Alexandre¹²³,Stefic Karl⁴,Marlet Julien⁴,Eymieux Sébastien⁴,Regue Hadrien³,Semanas Quentin³,d’Aubarede Constance⁵,Billaud Geneviève³,Laurent Frédéric⁶⁷,Gonzalez Claudia³,Mekki Yahia³,Valette Martine³,Bouscambert Maude³,Gaudy-Graffin Catherine⁴,Lina Bruno¹³,Morfin Florence¹³,Josset Laurence¹³,

Affiliation:

1. CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm,

2. These authors contributed equally to this article

3. Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France

4. Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France

5. Occupational Health and Medicine Department, Hospices Civils de Lyon, Lyon, France

6. Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France

7. CIRI - Centre International de Recherche en Infectiologie, Team Pathogenesis of staphylococcal infections Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France

Abstract

We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69–V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.

Publisher

European Centre for Disease Control and Prevention (ECDC)

Subject

Virology,Public Health, Environmental and Occupational Health,Epidemiology

Reference20 articles.

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