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; Pardis C Sabeti

doi:10.1038/s41467-020-17994-9

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

Nat Commun. 2020 Aug 17;11(1):4131. doi: 10.1038/s41467-020-17994-9.

Authors

Kayla G Barnes^#^{1

2

3}, Anna E Lachenauer^#^{4

5}, Adam Nitido^{6

7}, Sameed Siddiqui^{8

9}, Robin Gross¹⁰, Brett Beitzel¹¹, Katherine J Siddle^{8

12}, Catherine A Freije^{8

7}, Bonnie Dighero-Kemp¹⁰, Samar B Mehta^{8

13}, Amber Carter⁸, Jessica Uwanibe^{14

15}, Fehintola Ajogbasile^{14

15}, Testimony Olumade^{14

15}, Ikponmwosa Odia¹⁶, John Demby Sandi^{14

17}, Mambu Momoh^{14

17}, Hayden C Metsky^{8

18}, Chloe K Boehm⁸, Aaron E Lin^{8

7}, Molly Kemball^{8

12}, Daniel J Park⁸, Luis Branco¹⁹, Matt Boisen¹⁹, Brian Sullivan²⁰, Mihret F Amare^{21

22}, Abdulwasiu B Tiamiyu^{21

23}, Zahra F Parker^{21

22}, Michael Iroezindu^{21

23}, Donald S Grant^{17

24}, Kayvon Modjarrad²¹, Cameron Myhrvold^{8

12}, Robert F Garry^{19

25}, Gustavo Palacios¹¹, Lisa E Hensley¹⁰, Stephen F Schaffner^{8

26

12}, Christian T Happi^{26

14

15

16}, Andres Colubri^{8

12}, Pardis C Sabeti^{8

26

12

27}

Affiliations

¹ Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. kbarnes@broadinstitute.org.
² Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA. kbarnes@broadinstitute.org.
³ MRC-University of Glasgow Centre for Virus Research, Glasgow, UK. kbarnes@broadinstitute.org.
⁴ Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. annalach@stanford.edu.
⁵ Stanford University School of Medicine, Stanford, California, USA. annalach@stanford.edu.
⁶ Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, 02139, USA.
⁷ Ph.D. Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, 02115, USA.
⁸ Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
⁹ Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
¹⁰ Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA.
¹¹ Center for Genome Sciences, The United States Army Medical Research Institute for Infectious Disease, 1425 Porter Street, Fort Detrick, Maryland, 21702, USA.
¹² Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
¹³ Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.
¹⁴ African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
¹⁵ Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
¹⁶ Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
¹⁷ Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.
¹⁸ Department of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts, 02139, USA.
¹⁹ Zalgen Labs, Germantown, Maryland, USA.
²⁰ Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.
²¹ Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
²² Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA.
²³ Henry M. Jackson Foundation Medical Research International, Abuja, Nigeria.
²⁴ Ministry of Health and Sanitation, Freetown, Sierra Leone.
²⁵ Tulane University School of Medicine, New Orleans, Los Angeles, 70112, USA.
²⁶ Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA.
²⁷ Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

^# Contributed equally.

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.

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

Antibodies, Viral
Clustered Regularly Interspaced Short Palindromic Repeats / genetics
Ebolavirus / genetics
Ebolavirus / pathogenicity*
Hemorrhagic Fever, Ebola / diagnosis*
Hemorrhagic Fever, Ebola / virology
Lassa Fever / diagnosis*
Lassa Fever / virology
Lassa virus / genetics
Lassa virus / pathogenicity*

Substances

Antibodies, Viral

Abstract

Publication types

MeSH terms

Substances

Grants and funding