Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

Kayla G. Barnes (), Anna E. Lachenauer (), Adam Nitido, Sameed Siddiqui, Robin Gross, Brett Beitzel, Katherine J. Siddle, Catherine A. Freije, Bonnie Dighero-Kemp, Samar B. Mehta, Amber Carter, Jessica Uwanibe, Fehintola Ajogbasile, Testimony Olumade, Ikponmwosa Odia, John Demby Sandi, Mambu Momoh, Hayden C. Metsky, Chloe K. Boehm, Aaron E. Lin, Molly Kemball, Daniel J. Park, Luis Branco, Matt Boisen, Brian Sullivan, Mihret F. Amare, Abdulwasiu B. Tiamiyu, Zahra F. Parker, Michael Iroezindu, Donald S. Grant, Kayvon Modjarrad, Cameron Myhrvold, Robert F. Garry, Gustavo Palacios, Lisa E. Hensley, Stephen F. Schaffner, Christian T. Happi, Andres Colubri and Pardis C. Sabeti
Additional contact information
Kayla G. Barnes: Broad Institute of MIT and Harvard
Anna E. Lachenauer: Broad Institute of MIT and Harvard
Adam Nitido: Ragon Institute of MGH, MIT, and Harvard
Sameed Siddiqui: Broad Institute of MIT and Harvard
Robin Gross: National Institute of Allergy and Infectious Diseases, National Institutes of Health
Brett Beitzel: The United States Army Medical Research Institute for Infectious Disease
Katherine J. Siddle: Broad Institute of MIT and Harvard
Catherine A. Freije: Broad Institute of MIT and Harvard
Bonnie Dighero-Kemp: National Institute of Allergy and Infectious Diseases, National Institutes of Health
Samar B. Mehta: Broad Institute of MIT and Harvard
Amber Carter: Broad Institute of MIT and Harvard
Jessica Uwanibe: Redeemer’s University
Fehintola Ajogbasile: Redeemer’s University
Testimony Olumade: Redeemer’s University
Ikponmwosa Odia: Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital
John Demby Sandi: Redeemer’s University
Mambu Momoh: Redeemer’s University
Hayden C. Metsky: Broad Institute of MIT and Harvard
Chloe K. Boehm: Broad Institute of MIT and Harvard
Aaron E. Lin: Broad Institute of MIT and Harvard
Molly Kemball: Broad Institute of MIT and Harvard
Daniel J. Park: Broad Institute of MIT and Harvard
Luis Branco: Zalgen Labs
Matt Boisen: Zalgen Labs
Brian Sullivan: The Scripps Research Institute
Mihret F. Amare: Walter Reed Army Institute of Research
Abdulwasiu B. Tiamiyu: Walter Reed Army Institute of Research
Zahra F. Parker: Walter Reed Army Institute of Research
Michael Iroezindu: Walter Reed Army Institute of Research
Donald S. Grant: Kenema Government Hospital
Kayvon Modjarrad: Walter Reed Army Institute of Research
Cameron Myhrvold: Broad Institute of MIT and Harvard
Robert F. Garry: Zalgen Labs
Gustavo Palacios: The United States Army Medical Research Institute for Infectious Disease
Lisa E. Hensley: National Institute of Allergy and Infectious Diseases, National Institutes of Health
Stephen F. Schaffner: Broad Institute of MIT and Harvard
Christian T. Happi: Harvard T.H. Chan School of Public Health, Harvard University
Andres Colubri: Broad Institute of MIT and Harvard
Pardis C. Sabeti: Broad Institute of MIT and Harvard

Nature Communications, 2020, vol. 11, issue 1, 1-10

Abstract: Abstract Recent outbreaks of viral hemorrhagic fevers (VHFs), including Ebola virus disease (EVD) and Lassa fever (LF), highlight the urgent need for sensitive, deployable tests to diagnose these devastating human diseases. Here we develop CRISPR-Cas13a-based (SHERLOCK) diagnostics targeting Ebola virus (EBOV) and Lassa virus (LASV), with both fluorescent and lateral flow readouts. We demonstrate on laboratory and clinical samples the sensitivity of these assays and the capacity of the SHERLOCK platform to handle virus-specific diagnostic challenges. We perform safety testing to demonstrate the efficacy of our HUDSON protocol in heat-inactivating VHF viruses before SHERLOCK testing, eliminating the need for an extraction. We develop a user-friendly protocol and mobile application (HandLens) to report results, facilitating SHERLOCK’s use in endemic regions. Finally, we successfully deploy our tests in Sierra Leone and Nigeria in response to recent outbreaks.

Date: 2020
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DOI: 10.1038/s41467-020-17994-9

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