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

Antonin Bal; Gregory Destras; Alexandre Gaymard; Karl Stefic; Julien Marlet; Sébastien Eymieux; Hadrien Regue; Quentin Semanas; Constance d'Aubarede; Geneviève Billaud; Frédéric Laurent; Claudia Gonzalez; Yahia Mekki; Martine Valette; Maude Bouscambert; Catherine Gaudy-Graffin; Bruno Lina; Florence Morfin; Laurence Josset; COVID-Diagnosis HCL Study Group

doi:10.2807/1560-7917.ES.2021.26.3.2100008

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

Euro Surveill. 2021 Jan;26(3):2100008. doi: 10.2807/1560-7917.ES.2021.26.3.2100008.

Authors

Antonin Bal^{1

2

3}, Gregory Destras^{1

2

3}, Alexandre Gaymard^{1

2

3}, Karl Stefic⁴, Julien Marlet⁴, Sébastien Eymieux⁴, Hadrien Regue¹, Quentin Semanas¹, Constance d'Aubarede⁵, Geneviève Billaud¹, Frédéric Laurent^{6

7}, Claudia Gonzalez¹, Yahia Mekki¹, Martine Valette¹, Maude Bouscambert¹, Catherine Gaudy-Graffin⁴, Bruno Lina^{1

3}, Florence Morfin^{1

3}, Laurence Josset^{1

3}; COVID-Diagnosis HCL Study Group⁸

Collaborators

COVID-Diagnosis HCL Study Group:
Jean-Sébastien Casalegno, Emilie Frobert, Vanessa Escuret, Vinca Icard, Marion Jeannoel, Marie-Paule Milon, Christophe Ramière, Caroline Scholtès, Jean-Claude Tardy, Mary-Anne Trabaud, Isabelle Schuffenecker

Affiliations

¹ 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.
² These authors contributed equally to this article.
³ CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm.
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 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.
⁷ Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.
⁸ The members of the COVID-Diagnosis HCL Study Group are listed below.

PMID: 33478625
PMCID: PMC7848679
DOI: 10.2807/1560-7917.ES.2021.26.3.2100008

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.

Keywords: COVID-19, whole genome sequencing; SARS-CoV-2; spike protein, variants, deletion.

MeSH terms

Base Sequence*
COVID-19 / epidemiology*
France / epidemiology
Genome, Viral*
Humans
SARS-CoV-2 / genetics*
Sequence Deletion / genetics*
Spike Glycoprotein, Coronavirus / genetics*

Substances

Spike Glycoprotein, Coronavirus