Since the beginning of the Covid-19 pandemics, variants have emerged. Some of them display increased transmissibility and/or resistance to immune response. Most of the mutations involved in the functional adaptation are found in the Receptor Binding Module (RBM), close to the interface with the receptor ACE2. We thus developed a fast molecular assay to detect mutations in the RBM coding sequence. After amplification, the amplicon is heat-denatured and hybridized with an amplicon of reference. The presence of a mutation can be detected using a mismatch-specific endonuclease and the cleavage pattern is analysed by capillary electrophoresis. The method was validated on RNA of SARS-CoV-2 variants produced in vitro before being implemented for clinical samples. The assay showed 97.8% sensitivity and 97.8% specificity. The procedure can be set up for high throughput identification of the presence of mutations and serve as a first-line screening to select the samples for full genome sequencing.
Available online 21 October 2021, 103329