Eurosurv. Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France,

[tetano]

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[SUP]1,2,3[/SUP] , Gregory Destras[SUP]1,2,3[/SUP] , Alexandre Gaymard[SUP]1,2,3[/SUP] , Karl Stefic[SUP]4[/SUP] , Julien Marlet[SUP]4[/SUP] , S?bastien Eymieux[SUP]4[/SUP] , Hadrien Regue[SUP]1[/SUP] , Quentin Semanas[SUP]1[/SUP] , Constance d’Aubarede[SUP]5[/SUP] , Genevi?ve Billaud[SUP]1[/SUP] , Fr?d?ric Laurent[SUP]6,7[/SUP] , Claudia Gonzalez[SUP]1[/SUP] , Yahia Mekki[SUP]1[/SUP] , Martine Valette[SUP]1[/SUP] , Maude Bouscambert[SUP]1[/SUP] , Catherine Gaudy-Graffin[SUP]4[/SUP] , Bruno Lina[SUP]1,3[/SUP] , Florence Morfin[SUP]1,3[/SUP] , Laurence Josset[SUP]1,3[/SUP] , the COVID-Diagnosis HCL Study Group[SUP]8[/SUP]

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.

full article

https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.3.2100008#abstract_content