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Manning BJ, Khan WA, Peña JM, Fiore ES, Boisvert H, Tudino MC, Barney RE, Wilson MK, Singh S, Mowatt JA, Thompson HJ, Tsongalis GJ, Blake WJ. High-Throughput CRISPR-Cas13 SARS-CoV-2 Test. Clin Chem 2021; 68:172-180. [PMID: 34718481 DOI: 10.1093/clinchem/hvab238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND The ability to control the spread of COVID-19 continues to be hampered by a lack of rapid, scalable, and easily deployable diagnostic solutions. METHODS : We developed a diagnostic method based on CRISPR that can deliver sensitive, specific, and high-throughput detection of Sudden Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). The assay utilizes SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) for the qualitative detection of SARS-CoV-2 RNA and may be performed directly on a swab or saliva sample without nucleic acid extraction. The assay uses a 384-well format and provides results in less than one hour. RESULTS Assay performance was evaluated with 105 (55 negative, 50 positive) remnant SARS-CoV-2 specimens previously identified as positive using Food and Drug Administration emergency use authorized assays and re-tested with a modified version of the Centers for Disease Control and Prevention (CDC) RT-qPCR assay. When combined with magnetic bead-based extraction, the high throughput SHERLOCK SARS-CoV-2 assay was 100% concordant (n = 60) with the CDC RT-qPCR. When used with direct sample addition the high throughput assay was also 100% concordant with the CDC RT-qPCR direct method (n = 45). With direct saliva sample addition, the negative and positive percent agreements were 100% (15/15, 95% CI : 81.8-100%) and 88% (15/17, 95% CI : 63.6-98.5%), respectively, compared with results from a collaborating clinical laboratory. CONCLUSIONS This high throughput assay identifies SARS-CoV-2 from patient samples with or without nucleic acid extraction with high concordance to RT-qPCR methods. This test enables high complexity laboratories to rapidly increase their testing capacities with simple equipment.
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Affiliation(s)
- Brendan J Manning
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
| | - Wahab A Khan
- Department of Pathology and Laboratory Medicine, The Audrey and Theodore Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.,Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, 1 Medical Center Drive, Lebanon, NH, 03756, USA
| | - Jennifer M Peña
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
| | - Elizabeth S Fiore
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
| | - Heike Boisvert
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
| | - Marisa C Tudino
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
| | - Rachael E Barney
- Department of Pathology and Laboratory Medicine, The Audrey and Theodore Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Mary K Wilson
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
| | - Subha Singh
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
| | - Joel A Mowatt
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
| | - Hannah J Thompson
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
| | - Gregory J Tsongalis
- Department of Pathology and Laboratory Medicine, The Audrey and Theodore Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.,Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, 1 Medical Center Drive, Lebanon, NH, 03756, USA
| | - William J Blake
- R&D Department, Sherlock Biosciences, 40 Guest Street, 3rd Floor, Boston, MA, 02135, USA
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