Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform

• DOI: 10.1016/j.bios.2021.113857
• Publication Date: 2021-12-02T01:43:05Z
• Authors: Changsheng He; Cailing Lin; Guosheng Mo; Binbin Xi; An′an Li; Dongchao Huang; Yanbin Wan; Feng Chen; Yufeng Liang; Qingxia Zuo; Wanqing Xu; Dongyan Feng; Guanting Zhang; Liya Han; Changwen Ke; Hongli Du; Lizhen Huang
• Keywords: 0301 basic medicine; SARS-CoV-2; COVID-19; Biomolecules (q-bio.BM); Biosensing Techniques; Quantitative Biology - Quantitative Methods; Article; 3. Good health; 03 medical and health sciences; Quantitative Biology - Biomolecules; FOS: Biological sciences; Mutation; Humans; CRISPR-Cas Systems; Quantitative Methods (q-bio.QM)

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/$��$L). 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.<br/>39 pages, 6 figures<br/>