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 and Cameron Myhrvold ()
Additional contact information
Jon Arizti-Sanz: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Catherine A. Freije: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Alexandra C. Stanton: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Brittany A. Petros: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Chloe K. Boehm: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Sameed Siddiqui: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Bennett M. Shaw: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Gordon Adams: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Tinna-Solveig F. Kosoko-Thoroddsen: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Molly E. Kemball: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Jessica N. Uwanibe: Redeemer’s University
Fehintola V. Ajogbasile: Redeemer’s University
Philomena E. Eromon: Redeemer’s University
Robin Gross: National Institute of Allergy and Infectious Diseases, National Institutes of Health
Loni Wronka: National Biodefense Analysis and Countermeasures Center
Katie Caviness: National Biodefense Analysis and Countermeasures Center
Lisa E. Hensley: National Institute of Allergy and Infectious Diseases, National Institutes of Health
Nicholas H. Bergman: National Biodefense Analysis and Countermeasures Center
Bronwyn L. MacInnis: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Christian T. Happi: Redeemer’s University
Jacob E. Lemieux: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Pardis C. Sabeti: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard
Cameron Myhrvold: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard

Nature Communications, 2020, vol. 11, issue 1, 1-9

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-19097-x

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