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, Grégory Destras, Alexandre Gaymard, Karl Stéfic, Julien Marlet, Sébastien Eymieux, Hadrien Regue, Quentin Semanas, Constance d’Aubarede, Geneviève Billaud, Frédéric Laurent, Claudia González, Yahia Mekki, Martine Valette, Maude Bouscambert, Catherine Gaudy‐Graffin, Bruno Lina, Florence Morfin, Laurence Josset, the COVID-Diagnosis HCL Study Group
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.