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

doi:10.1101/2020.05.28.119131

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

bioRxiv [Preprint]. 2020 May 28:2020.05.28.119131. doi: 10.1101/2020.05.28.119131.

Authors

Jon Arizti-Sanz^{1

2}, Catherine A Freije^{1

3}, Alexandra C Stanton^{1

3}, Chloe K Boehm¹, Brittany A Petros^{1

2

4}, Sameed Siddiqui^{1

5}, Bennett M Shaw^{1

6}, Gordon Adams¹, Tinna-Solveig F Kosoko-Thoroddsen¹, Molly E Kemball¹, Robin Gross⁷, Loni Wronka⁸, Katie Caviness⁸, Lisa E Hensley⁷, Nicholas H Bergman⁸, Bronwyn L MacInnis^{1

9}, Jacob E Lemieux^{1

6}, Pardis C Sabeti^{1

9

10

11

12}, Cameron Myhrvold^{1

10

12}

Affiliations

¹ Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
² Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA.
³ Program in Virology, Harvard Medical School, Boston, MA, USA.
⁴ Harvard-MIT MD-PhD Program, Boston, MA, USA.
⁵ Computational and Systems Biology PhD program, MIT, Cambridge, MA, USA.
⁶ Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
⁷ Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA.
⁸ National Biodefense Analysis and Countermeasures Center, Fort Detrick, MD, USA.
⁹ Harvard T.H. Chan School of Public Health, Boston, MA, USA.
¹⁰ Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
¹¹ Howard Hughes Medical Institute, Chevy Chase, MD, USA.
¹² Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.

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.

Publication types

Preprint

Grants and funding

T32 GM007753/GM/NIGMS NIH HHS/United States