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Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2

View ORCID ProfileJon Arizti-Sanz, View ORCID ProfileCatherine A. Freije, View ORCID ProfileAlexandra C. Stanton, View ORCID ProfileChloe K. Boehm, View ORCID ProfileBrittany A. Petros, Sameed Siddiqui, View ORCID ProfileBennett M. Shaw, Gordon Adams, Tinna-Solveig F. Kosoko-Thoroddsen, Molly E. Kemball, Robin Gross, Loni Wronka, Katie Caviness, Lisa E. Hensley, Nicholas H. Bergman, Bronwyn L. MacInnis, Jacob E. Lemieux, Pardis C. Sabeti, View ORCID ProfileCameron Myhrvold
doi: https://doi.org/10.1101/2020.05.28.119131
Jon Arizti-Sanz
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
2Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
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Catherine A. Freije
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
3Program in Virology, Harvard Medical School, Boston, MA, USA
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Alexandra C. Stanton
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
3Program in Virology, Harvard Medical School, Boston, MA, USA
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Chloe K. Boehm
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
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  • ORCID record for Chloe K. Boehm
Brittany A. Petros
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
2Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
4Harvard-MIT MD-PhD Program, Boston, MA, USA
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Sameed Siddiqui
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
5Computational and Systems Biology PhD program, MIT, Cambridge, MA, USA
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Bennett M. Shaw
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
6Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
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  • ORCID record for Bennett M. Shaw
Gordon Adams
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
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Tinna-Solveig F. Kosoko-Thoroddsen
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
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Molly E. Kemball
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
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Robin Gross
7Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
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Loni Wronka
8National Biodefense Analysis and Countermeasures Center, Fort Detrick, MD, USA
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Katie Caviness
8National Biodefense Analysis and Countermeasures Center, Fort Detrick, MD, USA
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Lisa E. Hensley
7Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
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Nicholas H. Bergman
8National Biodefense Analysis and Countermeasures Center, Fort Detrick, MD, USA
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Bronwyn L. MacInnis
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
9Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Jacob E. Lemieux
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
6Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
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Pardis C. Sabeti
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
9Harvard T.H. Chan School of Public Health, Boston, MA, USA
10Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
11Howard Hughes Medical Institute, Chevy Chase, MD, USA
12Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
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Cameron Myhrvold
1Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
10Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
12Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
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  • For correspondence: cmyhrvol@broadinstitute.org
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Abstract

The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (SHERLOCK and HUDSON Integration to Navigate Epidemics), a sensitive and specific integrated diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We combine the steps of SHERLOCK into a single-step reaction and optimize HUDSON to accelerate viral inactivation in nasopharyngeal swabs and saliva. SHINE’s results can be visualized with an in-tube fluorescent readout — reducing contamination risk as amplification reaction tubes remain sealed — and interpreted by a companion smartphone application. We validate SHINE on 50 nasopharyngeal patient samples, demonstrating 90% sensitivity and 100% specificity compared to RT-PCR with a sample-to-answer time of 50 minutes. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

Competing Interest Statement

C.A.F., P.C.S., and C.M. are inventors on patent filings related to this work. J.E.L. consults for Sherlock Biosciences, Inc. P.C.S. is a co-founder of, shareholder in, and advisor to Sherlock Biosciences, Inc, as well as a Board member of and shareholder in Danaher Corporation.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2
Jon Arizti-Sanz, Catherine A. Freije, Alexandra C. Stanton, Chloe K. Boehm, Brittany A. Petros, Sameed Siddiqui, Bennett M. Shaw, Gordon Adams, Tinna-Solveig F. Kosoko-Thoroddsen, Molly E. Kemball, Robin Gross, Loni Wronka, Katie Caviness, Lisa E. Hensley, Nicholas H. Bergman, Bronwyn L. MacInnis, Jacob E. Lemieux, Pardis C. Sabeti, Cameron Myhrvold
bioRxiv 2020.05.28.119131; doi: https://doi.org/10.1101/2020.05.28.119131
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Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2
Jon Arizti-Sanz, Catherine A. Freije, Alexandra C. Stanton, Chloe K. Boehm, Brittany A. Petros, Sameed Siddiqui, Bennett M. Shaw, Gordon Adams, Tinna-Solveig F. Kosoko-Thoroddsen, Molly E. Kemball, Robin Gross, Loni Wronka, Katie Caviness, Lisa E. Hensley, Nicholas H. Bergman, Bronwyn L. MacInnis, Jacob E. Lemieux, Pardis C. Sabeti, Cameron Myhrvold
bioRxiv 2020.05.28.119131; doi: https://doi.org/10.1101/2020.05.28.119131

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