Rapid and Technically Simple Detection of SARS-CoV-2 Variants Using CRISPR Cas12 and Cas13

The worldwide proliferation of the SARS-CoV-2 virus in the past 3 years has allowed the virus to accumulate numerous mutations. Dangerous lineages have emerged one after another, each leading to a new wave of the pandemic. In this study, we have developed the THRASOS pipeline to rapidly discover lineage-specific mutation signatures and thus advise the development of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based diagnostic tests. We also optimized a strategy to modify loop-mediated isothermal amplification amplicons for downstream use with Cas12 and Cas13 for future multiplexing. The close ancestry of the BA.1 and BA.2 variants of SARS-CoV-2 (Omicron) made these excellent candidates for the development of a first test using this workflow. With a quick turnaround time and low requirements for laboratory equipment, the test we have created is ideally suited for settings such as mobile clinics lacking equipment such as Next-Generation Sequencers or Sanger Sequencers and the personnel to run these devices.

Automated summary

In this study, the THRASOS pipeline was developed to discover lineage-specific mutation signatures and guide the development of CRISPR-based diagnostic tests. Additionally, a strategy to modify loop-mediated isothermal amplification amplicons for use with Cas12 and Cas13 was optimized for future multiplexing. The BA.1 and BA.2 variants of SARS-CoV-2 (Omicron), which share close ancestry, were chosen as candidates for the first test using this workflow. The created test is ideal for settings such as mobile clinics lacking equipment and personnel for Next-Generation Sequencers or Sanger Sequencers.