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2020•Nature CommunicationsOpen access

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

Kayla G. Barnes, Anna E. Lachenauer, Adam D. Nitido, Sameed M. Siddiqui, Robin Gross, Brett F. Beitzel, Katherine J. Siddle, Catherine A. Freije, Bonnie Dighero-Kemp, Samar B. Mehta, Amber Carter, Jessica N. Uwanibe, Fehintola V. Ajogbasile, Testimony Jesupamilerin Olumade, Ikponmwosa Odia, John Demby Sandi, Mambu Momoh, Hayden C. Metsky, Chloe K. Boehm, Aaron E. Lin, Molly E. Kemball, Daniel J. Park, Luis M. Branco, Matthew L. Boisen, Brian Martin Sullivan, Mihret F. Amare, Abdulwasiu Bolaji Tiamiyu, Zahra Parker, Michael Onyebuchi Iroezindu, Donald Samuel Grant, Kayvon Modjarrad, Cameron Myhrvold, Robert F. Garry, Gustavo F. Palacios, Lisa E. Hensley, Stephen F. Schaffner, Christian Tientcha Happi, Andrés Colubri, Pardis Christine Sabeti

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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.

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What this paper is about

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.

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Available 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.

Key concepts: Lassa virus, Ebola virus, Lassa fever, Sierra leone, Viral hemorrhagic fever, Virology, Outbreak, CRISPR

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