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 Jan;26(3):2100008. 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.

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

MeSH terms

  • Base Sequence*
  • COVID-19 / epidemiology*
  • France / epidemiology
  • Genome, Viral*
  • Humans
  • SARS-CoV-2 / genetics*
  • Sequence Deletion / genetics*
  • Spike Glycoprotein, Coronavirus / genetics*


  • Spike Glycoprotein, Coronavirus