Use of the Biomark-based protocol to detect mutations associated with SARS-CoV-2 variants.

(A) Overview of the probes design used for the detection of two deletion mutations found in the Spike gene (H69-V70, top panel) and in the NSP6 gene (3675-SGF, bottom panel). Deletions are highlighted in yellow with both nucleotide at the 5’ and 3’ side shown in red and green respectively. Of note: for the H69-V70 mutation an A-to-G punctual deletion is shown in blue. Three mutant probes and one wild type probe were generated for the H69—V70 deletion (21765–21770) and one mutant and one wild type probes were generated for the 3675 –GSF deletion (11288–11296). The nucleotide numbering is based on the reference SARS-CoV-2 complete sequence (NCBI Reference Sequence: NC_045512.2). (B) Heatmap of Cq value from RT-qPCR using various combinations of primer/probes performed on 74 SARS-CoV-2 positive clinical samples. Cq scale range is shown on the right. Using the Biomark-based protocol, 11 positive samples for the mutation associated with the SARS-CoV-2 variants have been detected (on 74 positive clinical samples).