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

作者：He, Changsheng; Lin, Cailing; Mo, Guosheng; Xi, Binbin; Li, Anan; Huang, Dongchao; Wan, Yanbin; Chen, Feng; Liang, Yufeng; Zuo, Qingxia; Xu, Wanqing; Feng, Dongyan; Zhang, Guanting; Han, Liya; Ke, Changwen; Du, Hongli; Huang, Lizhen^*

来源：Biosensors and Bioelectronics, 2022, 198: 113857.

DOI：10.1016/j.bios.2021.113857

• CRISPR/Cas12
• RT-CORDS
• D614G
• N501Y
• 69/70 deletion
• SARS-CoV-2 variants

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/mu 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.

• 单位
  中山大学; 南方医科大学