Detection of SARS-CoV-2 and Its Mutated Variants Using RT-LAMP-CRISPR-Cas12a Platform

The global outbreak of coronavirus disease 19 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has raised significant global apprehension. Developing a rapid, efficient, sensitive, and accurate point-of-care detection method is imperative for curbing SARS-CoV-2 transmission. Here, we screened a sequence, designed a set of highly sensitive loop-mediated isothermal amplification primers (LAMP) and gRNA, and developed a user-friendly detection platform combining CRISPR-Cas12a and RT-LAMP technology to specifically detect SARS-CoV-2 and its 5 variants. Bioinformatics analysis and Cas12a-gRNA identification ensured sequence specificity, allowing us to identify SARS-CoV-2 mutations. We developed a method for the detection of SARS-CoV-2 using these primers in combination with LAMP amplification and CRISPR-Cas12a technology. This method is designed to detect SARS-CoV-2 (NC_045512), Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529). Additionally, it can differentiate SARS-CoV-2 from other coronaviruses. Quantitative analysis can be conducted by measuring fluorescence values, while qualitative analysis can be performed by observing fluorescence color point-of-care diagnosis changes with the naked eye. These results suggest that a set of novel sensitive LAMP primers and gRNA have been obtained to detect the extensive variants, and the RT-LAMP-CRISPR-Cas12a platform significantly facilitates point-of-care diagnosis, thereby halting the spread of SARS-CoV-2, thus contributing to COVID-19 prevention and control.