Two-step strategy for the identification of SARS-CoV-2 variants co-occurring with spike deletion H69-V70, Lyon, France, August to December 2020

Abstract The spike deletion H69-V70 (ΔH69/ΔV70) has been recently detected in a SARS-CoV-2 variant under investigation in England (VUI 202012/01) as well as in cluter-5 variant detected both in minks and humans in Denmark. Herein we report the implementation of a two-step strategy enabling to detect SARS-CoV-2 variants carrying H69-V70 deletion. We found that this deletion resulted in a false negative result for the spike target of a three-target RT-PCR assay (TaqPath kit). From August 3rd to December 20th, 59/9,266 (0.6%) of positive tests displayed a S negative profile (negative for S target and positive for N & ORF1ab targets). Among the 59 samples without detection of the S target, 36 were available for whole genome sequencing (WGS). The most frequent S mutations co-occurring with ΔH69/ΔV70 were S477N & D614G (21/36 samples). The co-occurrence of N439K and D614G mutations was found in 10/36 samples. The complete combination of S mutations detected in VUI 202012/01 or in cluster-5 variant was not found. The data presented herein emphasize that the TaqPath RT-PCR assay enables a rapid, large-scale screening of ΔH69/ΔV70 variants. Samples with S negative profiles should be further addressed to national referral laboratories for SARS-CoV-2 WGS. This 2-step strategy is currently being reinforced in France as national diagnostic platforms have mainly implemented the TaqPath RT-PCR kit.