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

This work was supported by the Fondo Supera COVID-19 from CRUE and Banco Santander (Grant COVCRISPIS, BOE-A-2020-7995, to GR), the CSIC PTI Salud Global (Grant SGL2021-03-040, to GR, and Grants 202020E292 and SGL2103034, to PDC) through the European Union−NextGeneration EU, the Fondo COVID-19 from the Instituto de Salud Carlos III (Grant COV20/00210, to PDC), and the Generalitat Valenciana (Grant SEJI/2020/ 011, to GR). PDC was supported by the Ramón y Cajal program (RYC2019-028015-I) and RMC by a predoctoral fellowship (PRE2019-088531), both from the Spanish Ministerio de Ciencia e Innovación.

Peer reviewed