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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.
Bal, Antonin; Destras, Gregory; Gaymard, Alexandre; Stefic, Karl; Marlet, Julien; Eymieux, Sébastien; Regue, Hadrien; Semanas, Quentin; d'Aubarede, Constance; Billaud, Geneviève; Laurent, Frédéric; Gonzalez, Claudia; Mekki, Yahia; Valette, Martine; Bouscambert, Maude; Gaudy-Graffin, Catherine; Lina, Bruno; Morfin, Florence; Josset, Laurence.
  • Bal A; 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.
  • Destras G; These authors contributed equally to this article.
  • Gaymard A; CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm.
  • Stefic K; 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.
  • Marlet J; These authors contributed equally to this article.
  • Eymieux S; CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm.
  • Regue H; 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.
  • Semanas Q; These authors contributed equally to this article.
  • d'Aubarede C; CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm.
  • Billaud G; Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France.
  • Laurent F; Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France.
  • Gonzalez C; Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France.
  • Mekki Y; 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.
  • Valette M; 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.
  • Bouscambert M; Occupational Health and Medicine Department, Hospices Civils de Lyon, Lyon, France.
  • Gaudy-Graffin C; 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.
  • Lina B; 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.
  • Morfin F; Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France.
  • Josset L; 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.
Euro Surveill ; 26(3)2021 01.
Article in English | MEDLINE | ID: covidwho-1041125
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 SN501Y in the VOC.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Base Sequence / Genome, Viral / Sequence Deletion / Spike Glycoprotein, Coronavirus / SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: 1560-7917.ES.2021.26.3.2100008

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Base Sequence / Genome, Viral / Sequence Deletion / Spike Glycoprotein, Coronavirus / SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: 1560-7917.ES.2021.26.3.2100008