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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
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View Affiliations Hide AffiliationsLaurence 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: . 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.