Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy

December 4, 2020

Fozouni P, Son S, Díaz de León Derby M, et al.

Cell

The authors of this paper used CRISPR diagnostic technology to develop a rapid and amplification-free diagnostic test for SARS-CoV-2 that can detect viral RNA directly from a nasal swab. Using the Cas13a protein, which can directly bind single-stranded RNA (ssRNA), researchers developed a CRISPR-Cas13 complex to target ssRNA. The addition of a fluorophore-quencher probe to the ssRNA strands allowed for quantification of Cas13a cleavage activity, where cleavage of the probe separates the quencher from the fluorophore and allows for fluorescence to occur. The CRISPR-Cas13a complex can directly detect viral RNA with a sensitivity of ~100 copies/uL in under 30 minutes, therefore removing the pre-amplification step that is often required for nucleic acid-based diagnostic tests. The experimental rate of Cas13a cleavage of ssRNA was compared and confirmed with Michaelis-Menten enzyme kinetics. This modeling also allowed for back-calculations to determine the target RNA concentration from the estimated concentration of activated Cas13a. Sensitivity of the assay was improved when combining CRISPR RNAs (crRNAs) to form several different complexes that could target different regions of viral RNA. Finally, results could be quantified with a mobile phone-based fluorescence microscope, increasing the accessibility of this technology to regions that lack robust laboratory equipment to perform diagnostic testing.

Fozouni P, Son S, Díaz de León Derby M, et al. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell 2020; 184: 1–11.

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