Author summary The recently discovered betacoronavirus severe acute respiratory syndrome (SARS)-CoV-2 has caused an outbreak of Coronavirus Disease 2019 (COVID-19) that rapidly developed into a global pandemic. The surging demand for rapid screening and identification of COVID-19 posts great diagnostic challenges. A lack of rapid and accurate molecular tools has hampered efficient public health responses to the viral threat. Here, we harnessed the unique collateral activity of programmable CRISPR/Cas13a to develop CRISPR-COVID, a rapid and sensitive diagnostic for SARS-CoV-2 infection, and compared it to sequencing-based metagenomic and RT-PCR-based assays in a clinical cohort. CRISPR-COVID demonstrated a sensitivity level of near single copy and was highly specific without cross reacting to related pathogens. CRISPR-COVID takes only 40 mins and requires no sophiscated thermo-cyclers, providing a valuable alternative to the conventional RT–PCR assay to circumvent the bottlenecks in assay turnaround time, equipment and reagent supplies for COVID-19 testing.
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