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 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.

Human-infecting coronaviruses

Species
SARS-related coronavirus
Full Severe acute respiratory syndrome-related coronavirus species. Includes SARS-CoV-2, SARS-CoV, and SARS-like CoVs.
Last updated on May 06, 2020.
Subspecies
SARS-CoV-2–related
SARS-CoV-2 and its closely-related bat and pangolin CoVs.
Last updated on May 07, 2020.
Subspecies
SARS-CoV-2
Cause of COVID-19. Excludes detection of RaTG13 genome and other bat and pangolin SARS-like CoVs. Strict subset of SARS-CoV-2–related.
Last updated on May 07, 2020.
Subspecies
SARS-CoV–related
SARS-CoV and its related bat CoVs.
Last updated on May 03, 2020.
Subspecies
SARS-CoV
Cause of SARS. Strict subset of SARS-CoV–related.
Last updated on May 03, 2020.
Species
HCoV-229E
Human coronavirus 229E. Common cause of mild respiratory illness.
Last updated on May 09, 2020.
Species
HCoV-HKU1
Human coronavirus HKU1. Common cause of mild respiratory illness.
Last updated on May 09, 2020.
Species
HCoV-NL63
Human coronavirus NL63. Common cause of mild respiratory illness.
Last updated on May 09, 2020.
Species
Betacoronavirus 1
Human coronavirus OC43 (HCoV-OC43), along with other subspecies. OC43 is a common cause of mild respiratory illness.
Last updated on May 09, 2020.
Species
MERS-CoV
Middle East respiratory syndrome-related coronavirus. Cause of MERS.
Last updated on May 09, 2020.

Orthomyxoviruses

Species
Influenza A virus
All known subtypes; segment 2. Influenza viruses cause flu.
Last updated on May 14, 2020.
Subspecies
Influenza A virus H1
All H1 subtypes (e.g., H1N1); segment 4. Intended for subtyping, alongside other designs.
Last updated on May 12, 2020.
Subspecies
Influenza A virus H3
All H3 subtypes (e.g., H3N2); segment 4. Intended for subtyping, alongside other designs.
Last updated on May 12, 2020.
Subspecies
Influenza A virus N1
All N1 subtypes (e.g., H1N1); segment 6. Intended for subtyping, alongside other designs.
Last updated on May 12, 2020.
Subspecies
Influenza A virus N2
All N2 subtypes (e.g., H3N2); segment 6. Intended for subtyping, alongside other designs.
Last updated on May 12, 2020.
Species
Influenza B virus
All known lineages; segment 1. Influenza viruses cause flu.
Last updated on May 14, 2020.

Paramyxoviruses

Species
HPIV-1
Human respirovirus 1. One cause of human parainfluenza, a common respiratory infection.
Last updated on Apr 16, 2020.
Species
HPIV-2
Human rubulavirus 2. One cause of human parainfluenza, a common respiratory infection.
Last updated on Apr 16, 2020.
Species
HPIV-3
Human respirovirus 3. One cause of human parainfluenza, a common respiratory infection.
Last updated on Apr 16, 2020.
Species
HPIV-4
Human rubulavirus 4. One cause of human parainfluenza, a common respiratory infection.
Last updated on Apr 16, 2020.

Picornaviruses

Species
Rhinovirus A
Rhinoviruses are the most common cause of the common cold.
Last updated on May 15, 2020.
Species
Rhinovirus B
Rhinoviruses are the most common cause of the common cold.
Last updated on May 15, 2020.
Species
Rhinovirus C
Rhinoviruses are the most common cause of the common cold.
Last updated on May 15, 2020.
Species
Enterovirus A
Non-polio enteroviruses are a common infection.
Last updated on May 15, 2020.
Species
Enterovirus B
Non-polio enteroviruses are a common infection.
Last updated on Jul 10, 2020.
Species
Enterovirus C
Non-polio enteroviruses are a common infection. Includes the poliovirus subtype.
Last updated on May 15, 2020.
Species
Enterovirus D
Non-polio enteroviruses are a common infection.
Last updated on May 15, 2020.

Pneumoviruses

Species
HRSV
Human orthopneumovirus. Common cause of respiratory illness.
Last updated on Feb 18, 2020.
Species
HMPV
Human metapneumovirus. Common cause of respiratory illness.
Last updated on Feb 18, 2020.

Other coronaviruses

Species
Alphacoronavirus 1
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Bat coronavirus 1A
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Bat coronavirus CDPHE15
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Bat coronavirus HKU10
Not known to cause human illness.
Last updated on May 09, 2020.
Species
BtRf-AlphaCoV/YN2012
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Coronavirus AcCoV-JC34
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Ferret coronavirus
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Lucheng Rn rat coronavirus
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Miniopterus bat coronavirus HKU8
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Mink coronavirus 1
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Myotis ricketti alphacoronavirus Sax-2011
Not known to cause human illness.
Last updated on May 09, 2020.
Species
NL63-related bat coronavirus strain BtKYNL63-9b
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Nyctalus velutinus alphacoronavirus SC-2013
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Porcine epidemic diarrhea virus
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Rhinolophus bat coronavirus HKU2
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Rhinolophus ferrumequinum alphacoronavirus HuB-2013
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Scotophilus bat coronavirus 512
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Wencheng Sm shrew coronavirus
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Bat Hp-betacoronavirus Zhejiang2013
Not known to cause human illness.
Last updated on May 09, 2020.
Species
China Rattus coronavirus HKU24
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Hedgehog coronavirus 1
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Murine coronavirus
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Pipistrellus bat coronavirus HKU5
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Rabbit coronavirus HKU14
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Rousettus bat coronavirus GCCDC1
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Rousettus bat coronavirus HKU9
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Tylonycteris bat coronavirus HKU4
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Bulbul coronavirus HKU11
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Common moorhen coronavirus HKU21
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Coronavirus HKU15
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Magpie-robin coronavirus HKU18
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Munia coronavirus HKU13
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Night heron coronavirus HKU19
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Sparrow coronavirus HKU17
Not known to cause human illness.
Last updated on May 09, 2020.
Species
White-eye coronavirus HKU16
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Wigeon coronavirus HKU20
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Avian coronavirus
Not known to cause human illness.
Last updated on May 09, 2020.
Species
Beluga whale coronavirus SW1
Not known to cause human illness.
Last updated on May 09, 2020.

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.