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. 2021 Jan;26(3):2100008.
doi: 10.2807/1560-7917.ES.2021.26.3.2100008.

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  1   2   3 , Gregory Destras  1   2   3 , Alexandre Gaymard  1   2   3 , Karl Stefic  4 , Julien Marlet  4 , Sébastien Eymieux  4 , Hadrien Regue  1 , Quentin Semanas  1 , Constance d'Aubarede  5 , Geneviève Billaud  1 , Frédéric Laurent  6   7 , Claudia Gonzalez  1 , Yahia Mekki  1 , Martine Valette  1 , Maude Bouscambert  1 , Catherine Gaudy-Graffin  4 , Bruno Lina  1   3 , Florence Morfin  1   3 , Laurence Josset  1   3 ; COVID-Diagnosis HCL Study Group  8
Collaborators, Affiliations

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 et al. Euro Surveill. 2021 Jan.

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.

Keywords: COVID-19, whole genome sequencing; SARS-CoV-2; spike protein, variants, deletion.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
(A) Amplification curvesa obtained with TaqPath COVID-19 RT-PCR kit for samples harbouring SARS-CoV-2 with nt deletion 21765–21770 in the spike gene and (B) pairwise sequence alignment from nt position 21758 to 21775 of a reference spike gene and a spike gene with the 21765–21770 deletion
Figure 2
Figure 2
Prevalence of the S negative profile (negative for S target and positive for N and ORF1ab targets) with TaqPath COVID-19 RT-PCR kit, Lyon, France, 3 August (week 32)–20 December (week 51) 2020 (n = 9,266 samples tested)
See this image and copyright information in PMC

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