Development of a rapid and simple test to detect the COVID-19 variants that can be used in remote areas and developing countries.

We have developed a rapid and simple test to detect COVID-19. It uses RNA extracted from a gargle sample. If present, millions of copies of a part of the SARS-Cov-2 are amplified at a fix temperature. Thus the test does not require an expensive temperature cycler normally used for RT-qPCR. The amplified SARS-CoV-2 RNA fragments are specifically cut by the Cas13a RNAse and a crRNA that detects a sequence of 28 nucleotides. Following this specific cut, the Cas13a cuts all the other RNAs present in the sample including a reporter RNA containing a fluorescein molecule on one end and a quencher on the other. When the reporter is intact and the fluorescein molecule is close to the quencher, the latter absorbs the fluorescent signal and the sample stays dark. However, following the cut of the reporter RNA by Cas13a, the positive samples become fluorescent green under a UV light. The proposed project objective is to modify our current test to detect and differentiate between the SARS-CoV-2 variants (London, South African and Brazilian variants) rapidly (under 2 hours) in remote regions of Canada and in developing countries. The modified test will use two enzymes simultaneously: Cas13, which cuts the RNA including a fluorescent green reporter RNA, and Cas12, which cuts DNA including a fluorescent yellow reporter DNA. The cutting of that reporter DNA leads to fluorescence at a different wavelength. The presence of one the fluorescence signals in two wells will serve to identify which variant is present in the sample. These fluorescent signals will be detected with a smartphone camera and the color combinations will be analyzed in large quantities by a cloud-based server to determine which variants are present and create anonymized reports. For this project, we have thus established collaborations with clinicians in several countries (Brazil, Maroc, Central African Republic, and Congo). In the future, the test will be modified to detect other viral and bacterial infections.