CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation

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Abstract

The novel respiratory virus SARS-CoV-2 is rapidly evolving across the world with the potential of increasing its transmission and the induced disease. Here, we applied the CRISPR-Cas12a system to detect, without the need of sequencing, SARS-CoV-2 genomes harboring the E484K mutation, first identified in the Beta variant and catalogued as an escape mutation. The E484K mutation creates a canonical protospacer adjacent motif for Cas12a recognition in the resulting DNA amplicon, which was exploited to obtain a differential readout. We analyzed a series of fecal samples from hospitalized patients in Valencia (Spain), finding one infection with SARS-CoV-2 harboring the E484K mutation, which was then confirmed by sequencing. Overall, these results suggest that CRISPR diagnostics can be a useful tool in epidemiology to monitor the spread of escape mutations.

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Marqués, M. C., Ruiz, R., Montagud-Martínez, R., Márquez-Costa, R., Albert, S., Domingo-Calap, P., & Rodrigo, G. (2021). CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. ACS Synthetic Biology, 10(12), 3595–3599. https://doi.org/10.1021/acssynbio.1c00323

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