Sherlock™ CRISPR SARS-CoV-2 kit

The Sherlock™ CRISPR SARS-CoV-2 kit it is the first US FDA emergency use authorization (EUA) CRISPR-based diagnostic test intended for the qualitative detection of nucleic acid from SARS-CoV-2. This kit provides specific and sensitive detection of the SARS-CoV-2 virus in upper respiratory tract samples from individuals suspected of having COVID-19 by their healthcare provider.

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This product is available for purchase only in the USA.

Sherlock™ CRISPR SARS-CoV-2 kit

  • Faster than PCR: approximately 1-hour assay time
  • Add hundreds of tests per day to current lab volume
  • 100% concordance in EUA clinical evaluation
  • Minimal footprint: uses standard laboratory equipment
  • CRISPR SHERLOCK technology: proven highly sensitive (limit of detection: 6.75 copies/µL from viral transport medium)
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Product Details

The Sherlock™ CRISPR SARS-CoV-2 kit is designed to detect fragments in the Open Reading Frame (ORF1ab) gene and the Nucleocapsid (N) gene of the SARS-CoV-2 virus. An internal control targets the human RNase P POP7 gene to confirm clinical sample extraction in the absence of a positive SARS-CoV-2 result.

The assay (Figure 1) is comprised of two steps. Step one is reverse transcription, loop mediated isothermal amplification (RT-LAMP), where targeted SARS-CoV-2 genomic RNA is reverse transcribed to DNA then amplified by a strand-displacing DNA polymerase. Step two involves transcription of the amplified DNA to activate collateral cleavage activity of a CRISPR complex programmed to the target RNA sequence. During the second step, cleavage of nucleic acid reporters results in a fluorescent readout detectable by a standard plate reader.

Figure 1. Schematic of the Sherlock method. In brief, nucleic acids are extracted from patient specimens (sample prep). RT-LAMP followed by transcription is used to amplify SARS-CoV-2 targets (amplification). In the presence of viral targets, CRISPR-Cas13 ribonucleoproteins are activated (detection). The resulting cleavage by the Cas enzyme of nucleic acid reporters generates fluorescent signals detected by a plate reader (output). (Figure courtesy of Sherlock Biosciences.)

Safety, legal, quality, & usage

  • This test has not been cleared or approved by the U.S. Food and Drug Administration (FDA)
  • This test has been authorized by the U.S. Food and Drug Administration (FDA) under an Emergency Use Authorization (EUA) issued to Sherlock Biosciences on May 6, 2020 for use by authorized laboratories
  • This test has been authorized only for the detection of nucleic acid from SARS-CoV-2, not for any other viruses or pathogens
  • This test is only authorized for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in vitro diagnostics for detection and/or diagnosis of COVID-19 under Section 564(b)(1) of the Act, 21 U.S.C. § 360bbb-3(b)(1), unless the authorization is terminated or revoked sooner.
  • This product is covered by one or more patents, trademarks and/or copyrights owned or controlled by Sherlock Biosciences, Inc. (“Sherlock”), Eiken Chemical Co., Ltd., the Broad Institute, Inc., and Sherlock’s other partners. Additional details are available here.

Performance

The Sherlock kit is highly sensitive

To determine the Limit of Detection (LoD), limiting dilutions of quantified, extracted genomic RNA were spiked into a clinical matrix composed of pooled nasopharyngeal swabs after the initial lysis step. The LoD for the Sherlock CRISPR SARS-CoV-2 kit was determined to be the lowest concentration of genomic viral RNA (copies/µL of Viral Transport Media) at which ≥95% of all replicates tested were positive. As the assay contains two SARS-CoV-2 targets, ORF1ab and Nucleocapsid (N), the LoD for each target was independently determined and confirmed. The LoD claimed for the kit is the higher of the two values: 6.75 copies/µL VTM. Confirmatory LoD testing is demonstrated in Table 1. For more information on how the LoD was determined, refer to the Sherlock SARS-CoV-2 kit Instructions for Use in the Resources section. (Data courtesy of Sherlock Biosciences.)

Table 1. Confirmatory LoD testing.
TargetViral copies in sample (copies/µL VTM)Number of samplesNumber detectedDetection rate (%)
ORF1ab4.5201785
ORF1ab6.75201995
N0.9201785
N1.352020100

The Sherlock kit showed 100% concordance in EUA clinical evaluation

The clinical evaluation was performed on 30 contrived positive and 30 contrived negative nasopharyngeal specimens. Positive samples were contrived by spiking with quantitated SARS-CoV-2 viral genomic RNA to a concentration of 2X LoD (20 specimens), 3X LoD (5 specimens), or 5X LoD (5 specimens). The samples were randomized, then processed using the Sherlock CRISPR SARS-CoV-2 kit workflow. The results, as presented in Table 2, showed 100% agreement with the expected results for both the positive and negative specimens. For more information on how the clinical evaluation was performed, refer to the Sherlock SARS-CoV-2 kit Instructions for Use in the Resources section. (Data courtesy of Sherlock Biosciences.)

Table 2. Contrived clinical sample evaluation.
Sample concentrationNumber of samplesNumber detected% agreement (95% confidence interval)
5X LoD55100% (NA*)
3X LoD55100% (NA*)
2X LoD2020100% (83.9–100%)
Negative specimens300100% (88.6–100%)

* NA = not applicable, confidence intervals not calculated for sample sizes of 5 or less

Resources

Citations

  1. Gootenberg JS, Abudayyeh OO, et al. (2018) Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360(6387):439–444.
  2. Myhrvold C, Freije CA, et al. (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360(6387):444–448.
  3. Gootenberg JS, Abudayyeh OO, et al. (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356(6336):438–442.
  4. Abudayyeh OO, Gootenberg JS, et al. (2016) C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353(6299):aaf5573.
  5. Abudayyeh, O.O. et al. (2019). Nucleic acid detection of plant genes using CRISPR-Cas13. The CRISPR Journal 2(3):165–171.

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