SARS-CoV-2 detection with type I-A CRISPR “FALCON” system

CRISPR-Cas systems are currently applied in the detection of infectious diseases as a rapid and accurate alternative for the traditional RT-PCR (reverse-transcription polymerase chain reaction) test. The type I-A CRISPR-Cas nucleic acid detection system has been proven to achieve efficient detection through a 15-minute one-pot reaction at 85°C. For this project, a type I-A system “FALCON” (Fast Agent in Limited COVID Nucleic acid detection) was created to detect SARS-CoV-2 and its variants. The system’s guide RNA is designed with the N gene of SARS-CoV-2. When tested with samples containing SARS-CoV-2 pseudovirus, the system’s embedded Cas3 enzyme is activated upon guide RNA recognition and collaterally cleaves FQ (fluorophore-quencher) reporters, producing a fluorescent sample where the amount of fluorescence is proportional to the viral load. In addition, FALCON’s results are highly consistent with those of RT-PCR but requires much less instrumentation and shorter testing time, and can differentiate among virus variants. FALCON can be developed into commercial SARS-CoV-2 self-testing kits, or used in detection and differentiation of other diseases with a modified guide RNA.