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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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

Edité par CCSD ; European Centre for Disease Prevention and Control -

International audience. 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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