Rapid system to detect the main variants of SARS-CoV-2 in biological specimens

Since its appearance in late 2019, SARS-CoV-2 has been reported to acquire substitutions more slowly than other RNA viruses, but its tendency to manifest recurrent deletions in the spike glycoprotein exceeds this slow replacement rate. To date, deletion variants have been identified in many countries, some of which are transmitted efficiently and also present several lineages. The rapid identification of such variants is paramount to quickly implement containment measures. We developed a novel assay using traditional real-time PCR to detect the main reported variants of the spike gene of SARS CoV-2. Primers and probes were designed to detect the following deletions and mutations as well as to cover all lineages known to date (B.1.617, B.1.617.1, B.1.617.2, B.1.617.3 and B.1.618): 69:70 and 144:145 deletions, which denote the UK variant (VOC 202012/01); 242:244 deletion, which identifies the South African variant; Δ3675:3677 deletion in the ORF1a gene, which denotes the Brazilian variant; and P681R mutation as well as 145:146 and 157:158 deletions, which identify the Indian variant. Our assay will help clinical microbiologists and clinicians to rapidly recognize the presence of variants in biological samples (particularly nasopharyngeal swabs), and it may also be useful for epidemiological purposes in the early selection for successive tracing of patients harbouring virus variants that may be more diffusive and/or not responsive to vaccines.