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

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. LinMolly 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

Research output: Contribution to journal › Article › peer-review

113 Scopus citations

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.

Original language	English (US)
Article number	4131
Journal	Nature communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-17994-9
State	Published - Dec 1 2020
Externally published	Yes

All Science Journal Classification (ASJC) codes

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/s41467-020-17994-9

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Barnes, K. G., Lachenauer, A. E., Nitido, A., Siddiqui, S., Gross, R., Beitzel, B., Siddle, K. J., Freije, C. A., Dighero-Kemp, B., Mehta, S. B., Carter, A., Uwanibe, J., Ajogbasile, F., Olumade, T., Odia, I., Sandi, J. D., Momoh, M., Metsky, H. C., Boehm, C. K., ... Sabeti, P. C. (2020). Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time. Nature communications, 11(1), Article 4131. https://doi.org/10.1038/s41467-020-17994-9

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

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{\textquoteright}s use in endemic regions. Finally, we successfully deploy our tests in Sierra Leone and Nigeria in response to recent outbreaks.",

author = "Barnes, {Kayla G.} and Lachenauer, {Anna E.} and Adam Nitido and Sameed Siddiqui and Robin Gross and Brett Beitzel and Siddle, {Katherine J.} and Freije, {Catherine A.} and Bonnie Dighero-Kemp and Mehta, {Samar B.} and Amber Carter and Jessica Uwanibe and Fehintola Ajogbasile and Testimony Olumade and Ikponmwosa Odia and Sandi, {John Demby} and Mambu Momoh and Metsky, {Hayden C.} and Boehm, {Chloe K.} and Lin, {Aaron E.} and Molly Kemball and Park, {Daniel J.} and Luis Branco and Matt Boisen and Brian Sullivan and Amare, {Mihret F.} and Tiamiyu, {Abdulwasiu B.} and Parker, {Zahra F.} and Michael Iroezindu and Grant, {Donald S.} and Kayvon Modjarrad and Cameron Myhrvold and Garry, {Robert F.} and Gustavo Palacios and Hensley, {Lisa E.} and Schaffner, {Stephen F.} and Happi, {Christian T.} and Andres Colubri and Sabeti, {Pardis C.}",

note = "Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

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doi = "10.1038/s41467-020-17994-9",

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Barnes, KG, Lachenauer, AE, Nitido, A, Siddiqui, S, Gross, R, Beitzel, B, Siddle, KJ, Freije, CA, Dighero-Kemp, B, Mehta, SB, Carter, A, Uwanibe, J, Ajogbasile, F, Olumade, T, Odia, I, Sandi, JD, Momoh, M, Metsky, HC, Boehm, CK, Lin, AE, Kemball, M, Park, DJ, Branco, L, Boisen, M, Sullivan, B, Amare, MF, Tiamiyu, AB, Parker, ZF, Iroezindu, M, Grant, DS, Modjarrad, K, Myhrvold, C, Garry, RF, Palacios, G, Hensley, LE, Schaffner, SF, Happi, CT, Colubri, A & Sabeti, PC 2020, 'Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time', Nature communications, vol. 11, no. 1, 4131. https://doi.org/10.1038/s41467-020-17994-9

TY - JOUR

T1 - Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time

AU - Barnes, Kayla G.

AU - Lachenauer, Anna E.

AU - Nitido, Adam

AU - Siddiqui, Sameed

AU - Gross, Robin

AU - Beitzel, Brett

AU - Siddle, Katherine J.

AU - Freije, Catherine A.

AU - Dighero-Kemp, Bonnie

AU - Mehta, Samar B.

AU - Carter, Amber

AU - Uwanibe, Jessica

AU - Ajogbasile, Fehintola

AU - Olumade, Testimony

AU - Odia, Ikponmwosa

AU - Sandi, John Demby

AU - Momoh, Mambu

AU - Metsky, Hayden C.

AU - Boehm, Chloe K.

AU - Lin, Aaron E.

AU - Kemball, Molly

AU - Park, Daniel J.

AU - Branco, Luis

AU - Boisen, Matt

AU - Sullivan, Brian

AU - Amare, Mihret F.

AU - Tiamiyu, Abdulwasiu B.

AU - Parker, Zahra F.

AU - Iroezindu, Michael

AU - Grant, Donald S.

AU - Modjarrad, Kayvon

AU - Myhrvold, Cameron

AU - Garry, Robert F.

AU - Palacios, Gustavo

AU - Hensley, Lisa E.

AU - Schaffner, Stephen F.

AU - Happi, Christian T.

AU - Colubri, Andres

AU - Sabeti, Pardis C.

PY - 2020/12/1

Y1 - 2020/12/1

N2 - 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.

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

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