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

• Published in: Euro surveillance : bulletin européen sur les maladies transmissibles Vol. 26; no. 3; p. 1
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: Sweden Centre Europeen pour la Surveillance Epidemiologique du SIDA (European Centre for the Epidemiological Monitoring of AIDS) 21.01.2021; European Centre for Disease Prevention and Control; European Centre for Disease Prevention and Control (ECDC)
• Subjects: Base Sequence; COVID-19 - epidemiology; France - epidemiology; Genome, Viral; Human health and pathology; Humans; Infectious diseases; Life Sciences; Medical screening; Mutation; Rapid Communication; SARS-CoV-2 - genetics; Sequence Deletion - genetics; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - genetics; France; COVID-19, whole genome sequencing; spike protein, variants, deletion; SARS-CoV-2; COVID-19; whole genome sequencing; variants; deletion; spike protein
• ISSN: 1560-7917; 1025-496X; 1560-7917; 1025-496X
• DOI: 10.2807/1560-7917.ES.2021.26.3.2100008

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.