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

Jon Arizti-Sanz; Catherine A Freije; Alexandra C Stanton; Brittany A Petros; Chloe K Boehm; Sameed Siddiqui; Bennett M Shaw; Gordon Adams; Tinna-Solveig F Kosoko-Thoroddsen; Molly E Kemball; Jessica N Uwanibe; Fehintola V Ajogbasile; Philomena E Eromon; Robin Gross; Loni Wronka; Katie Caviness; Lisa E Hensley; Nicholas H Bergman; Bronwyn L MacInnis; Christian T Happi; Jacob E Lemieux; Pardis C Sabeti; Cameron Myhrvold

doi:10.1038/s41467-020-19097-x

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

Nat Commun. 2020 Nov 20;11(1):5921. doi: 10.1038/s41467-020-19097-x.

Authors

Jon Arizti-Sanz^{1

2}, Catherine A Freije^{1

3}, Alexandra C Stanton^{1

3}, Brittany A Petros^{1

2

4}, Chloe K Boehm¹, Sameed Siddiqui^{1

5}, Bennett M Shaw^{1

6}, Gordon Adams¹, Tinna-Solveig F Kosoko-Thoroddsen¹, Molly E Kemball¹, Jessica N Uwanibe^{7

8}, Fehintola V Ajogbasile^{7

8}, Philomena E Eromon⁷, Robin Gross⁹, Loni Wronka¹⁰, Katie Caviness¹⁰, Lisa E Hensley⁹, Nicholas H Bergman¹⁰, Bronwyn L MacInnis^{1

11}, Christian T Happi^{7

8

11}, Jacob E Lemieux^{1

6}, Pardis C Sabeti^{1

11

12

13

14}, Cameron Myhrvold^{15

16

17

18}

Affiliations

¹ Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, 02142, USA.
² Harvard-MIT Program in Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
³ Program in Virology, Harvard Medical School, Boston, MA, 02115, USA.
⁴ Harvard/MIT MD-PhD Program, Boston, MA, 02139, USA.
⁵ Computational and Systems Biology PhD Program, MIT, Cambridge, MA, 02139, USA.
⁶ Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, 55 Fruit Street Gray 730, Boston, MA, 02114, USA.
⁷ African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
⁸ Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
⁹ Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA.
¹⁰ National Biodefense Analysis and Countermeasures Center, Fort Detrick, MD, 21702, USA.
¹¹ Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA.
¹² Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
¹³ Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
¹⁴ Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
¹⁵ Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, 02142, USA. cmyhrvol@broadinstitute.org.
¹⁶ Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA. cmyhrvol@broadinstitute.org.
¹⁷ Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA. cmyhrvol@broadinstitute.org.
¹⁸ Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. cmyhrvol@broadinstitute.org.

Abstract

The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. 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-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Betacoronavirus / isolation & purification*
Biological Assay
COVID-19
CRISPR-Associated Proteins / metabolism*
Coronavirus Infections / diagnosis
Coronavirus Infections / virology
Fluorescence
Humans
Molecular Diagnostic Techniques / methods*
Pandemics
Pneumonia, Viral / diagnosis
Pneumonia, Viral / virology
SARS-CoV-2

Substances

CRISPR-Associated Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding