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

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

• Comprehensive: Designs are effective against variable targets because ADAPT considers the full spectrum of their known genomic diversity.
• Sensitive: ADAPT uses a model to predict detection activity across targeted genomic diversity, trained from ~19,000 guide-target pairs (based on LwaCas13a activity only).
• Specific: Designs have high predicted specificity to their species or subspecies, allowing them to be grouped into panels that are accurate in distinguishing related taxa.

More information about ADAPT is available in our publication in Nature Biotechnology. ADAPT is available through a web interface and a software package on GitHub.

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

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.