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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
- Antonin Bal1,2,3 , Gregory Destras1,2,3 , Alexandre Gaymard1,2,3 , Karl Stefic4 , Julien Marlet4 , Sébastien Eymieux4 , Hadrien Regue1 , Quentin Semanas1 , Constance d’Aubarede5 , Geneviève Billaud1 , Frédéric Laurent6,7 , Claudia Gonzalez1 , Yahia Mekki1 , Martine Valette1 , Maude Bouscambert1 , Catherine Gaudy-Graffin4 , Bruno Lina1,3 , Florence Morfin1,3 , Laurence Josset1,3 , the COVID-Diagnosis HCL Study Group8
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View Affiliations Hide AffiliationsAffiliations: 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 U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS 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 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 belowLaurence Jossetlaurence.josset chu-lyon.fr
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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 SchuffeneckerView Citation Hide Citation
Citation style for this article: 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, the COVID-Diagnosis HCL Study Group. 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;26(3):pii=2100008. https://doi.org/10.2807/1560-7917.ES.2021.26.3.2100008 Received: 05 Jan 2021; Accepted: 21 Jan 2021
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.

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References
-
European Centre for Disease Prevention and Control (ECDC). ECDC to assess risk associated with spread of SARS-CoV-2 in mink farms. Stockholm: ECDC; 2020. [Accessed 8 Nov 2020]. Available from: https://www.ecdc.europa.eu/en/news-events/ecdc-assess-risk-associated-spread-sars-cov-2-mink-farms
-
World Health Organization (WHO). SARS-CoV-2 mink-associated variant strain – Denmark. Geneva: WHO. [Accessed 25 Nov 2020]. Available from: http://www.who.int/csr/don/06-november-2020-mink-associated-sars-cov2-denmark/en/
-
Lassaunière R, Fonager J, Rasmussen M, Frische A, Polacek Strandh C, Bruun Rasmussen T, et al. Working paper on SARS-CoV-2 spike mutations arising in Danish mink, their spread to humans and neutralization data. Copenhagen: Statens Serum Institut. Available from: https://files.ssi.dk/Mink-cluster-5-short-report_AFO2
-
Kemp SA, Datir RP, Collier DA, Ferreira I, Carabelli A, Harvey W, et al. Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion ΔH69/ΔV70. bioRxiv. 2020:2020.12.14.422555; (Preprint). https://doi.org/10.1101/2020.12.14.422555
-
Thomson EC, Rosen LE, Shepherd JG, Spreafico R, Filipe A da S, Wojcechowskyj JA, et al. The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. bioRxiv. 2020:2020.11.04.355842.(Preprint). https://doi.org/10.1101/2020.11.04.355842
-
Andrew Rambaut, Nick Loman, Oliver Pybus, Wendy Barclay, Jeff Barrett, Alesandro Carabelli, Tom Connor, Tom Peacock, David L Robertson, Erik Volz, on behalf of COVID-19 Genomics Consortium UK (CoG-UK). Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological.org. [Accessed 21 Dec 2020]. Available from: https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563/1
-
Bal A, Destras G, Gaymard A, Bouscambert-Duchamp M, Valette M, Escuret V, et al. Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del). Clin Microbiol Infect. 2020;26(7):960-2. https://doi.org/10.1016/j.cmi.2020.03.020 PMID: 32234449
-
Singer J, Gifford R, Cotten M, Robertson D. CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation. 2020. doi: https://doi.org/10.20944/preprints202006.0225.v1 .
-
Charre C, Ginevra C, Sabatier M, Regue H, Destras G, Brun S, et al. Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation. Virus Evol. 2020;6(2):veaa075. https://doi.org/10.1093/ve/veaa075 PMID: 33318859
-
World Health Organization (WHO). Molecular assays to diagnose COVID-19: Summary table of available protocols. Geneva: WHO; 24 January 2020. Available from: https://www.who.int/publications/m/item/molecular-assays-to-diagnose-covid-19-summary-table-of-available-protocols
-
Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi JC, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. eLife. 2020;9:e61312. https://doi.org/10.7554/eLife.61312 PMID: 33112236
-
Baum A, Fulton BO, Wloga E, Copin R, Pascal KE, Russo V, et al. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science. 2020;369(6506):1014-8. https://doi.org/10.1126/science.abd0831 PMID: 32540904
-
Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KHD, Dingens AS, et al. Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding. Cell. 2020;182(5):1295-1310.e20. https://doi.org/10.1016/j.cell.2020.08.012 PMID: 32841599
-
Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, et al. Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data. medRxiv. 2020: 2020.12.30.20249034. (Preprint). https://doi.org/ https://doi.org/10.1101/2020.12.30.20249034
-
Kemp SA, Collier DA, Datir R, Gayed S, Jahun A, Hosmillo M, et al. Neutralising antibodies drive Spike mediated SARS-CoV-2 adaptation. medRxiv. 2020:2020.12.05.20241927. (Preprint). https://doi.org/10.1101/2020.12.05.20241927
-
Soh WT, Liu Y, Nakayama EE, Ono C, Torii S, Nakagami H, et al. The N-terminal domain of spike glycoprotein mediates SARS-CoV-2 infection by associating with L-SIGN and DC-SIGN. bioRxiv. 2020:2020.11.05.369264. (Preprint). doi: https://doi.org/10.1101/2020.11.05.369264
-
Chi X, Yan R, Zhang J, Zhang G, Zhang Y, Hao M, et al. A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science. 2020;369(6504):650-5. https://doi.org/10.1126/science.abc6952 PMID: 32571838
-
McCarthy KR, Rennick LJ, Nambulli S, Robinson-McCarthy LR, Bain WG, Haidar G, et al. Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape. bioRxiv. 2020:2020.11.19.389916. (Preprint). https://doi.org/10.1101/2020.11.19.389916
-
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv. 2020:2020.12.21.20248640. (Preprint). https://doi.org/ https://doi.org/10.1101/2020.12.21.20248640
-
Public Health England (PHE). Investigation of novel SARS-COV-2 variant. Variant of Concern 202012/01. London: PHE. Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/947048/Technical_Briefing_VOC_SH_NJL2_SH2.pdf

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