Assay designs for CRISPR-based detection of SARS-CoV-2 and related viruses

All nucleic acid detection assays are designed by ADAPT to be:

More information on these designs, including a protocol, is available in our February, 2020 paper on bioRxiv.

More information on ADAPT is available in our November, 2020 preprint on bioRxiv. ADAPT is available on GitHub.

Each design option consists of RPA primers and LwaCas13a crRNAs. The crRNAs (not primers) are designed to be specific because these perform the detection. These design options are generated computationally and fully automatically. We have not experimentally validated them, except for one SARS-CoV-2 assay. They are intended for research-use only.


Select one or multiple taxa below for a single assay or multiplex panel.


Taxonomies here (except SARS-CoV-1 and SARS-like) are based on NCBI's Taxonomy Database, which itself is kept up-to-date with ICTV taxonomy. Genomic data from NCBI's GenBank informed all of these designs, and data from GISAID informed the SARS-CoV-2 designs. All of these designs rely heavily on sequencing that other groups have performed and the genomes they have shared, and we are thankful to them for sharing data.

This website was created by Hayden Metsky in collaboration with others from the Sabeti lab. Please email hmetsky@broadinstitute.org with questions or comments.