Abstract
The increasing prevalence of SARS-CoV-2 variants with spike mutations has raised concerns owing to higher transmission rates, disease severity, and escape from neutralizing antibodies. Rapid and accurate detection of SARS-CoV-2 variants provides crucial information concerning the outbreaks of SARS-CoV-2 variants and possible lines of transmission. This information is vital for infection prevention and control. We used a Cas12a-based RT-PCR combined with CRISPR on-site rapid detection system (RT-CORDS) platform to detect the key mutations in SARS-CoV-2 variants, such as 69/70 deletion, N501Y, and D614G. We used type-specific CRISPR RNAs (crRNAs) to identify wild-type (crRNA-W) and mutant (crRNA-M) sequences of SARS-CoV-2. We successfully differentiated mutant variants from wild-type SARS-CoV-2 with a sensitivity of 10 -17 M (approximately 6 copies/μL). The assay took just 10 min with the Cas12a/crRNA reaction after a simple RT-PCR using a fluorescence reporting system. In addition, a sensitivity of 10 -16 M could be achieved when lateral flow strips were used as readouts. The accuracy of RT-CORDS for SARS-CoV-2 variant detection was 100% consistent with the sequencing data. In conclusion, using the RT-CORDS platform, we accurately, sensitively, specifically, and rapidly detected SARS-CoV-2 variants. This method may be used in clinical diagnosis.
Keywords: 69/70 deletion; CRISPR/Cas12; D614G; N501Y; RT-CORDS; SARS-CoV-2 variants.
【저자키워드】 SARS-CoV-2 variants, N501Y, D614G, 69/70 deletion, CRISPR/Cas12, RT-CORDS, 【초록키워드】 SARS-CoV-2, Mutation, Neutralizing antibodies, disease severity, variant, SARS-CoV-2 variant, Transmission, RT-PCR, RNA, Prevalence, CRISPR, lateral flow strip, sensitivity, Accuracy, SARS-CoV-2 variants, outbreak, spike mutation, N501Y, Infection prevention, Rapid, Deletion, D614G, spike mutations, mutant, information, Clinical diagnosis, platform, Prevention and control, sequence, wild-type SARS-CoV-2, wild-type, sequencing data, transmission rates, detection system, identify, detect, addition, raised, provide, were used, concerning, 【제목키워드】 Rapid, SARS-CoV-2 mutation, platform,