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

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74 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
Physics and Astronomy(all)
Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)

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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

@article{4d17aa4f4e3a4265949410470bbe3f7a,

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 = "Funding Information: Opinions, interpretations, conclusions, and recommendations are those of the authors and are not necessarily endorsed by the United States Army or the National Institute of Health. We thank the staff of the Joint West Africa Research Group, the Walter Reed Army Institute of Research, the Henry M. Jackson Foundation for the Advancement of Military Medicine, and the U.S. Embassy in Abuja, Nigeria, for their collaborative support and our colleagues at the Irrua Specialist Teaching Hospital, Nigeria, and Kenema Government Hospital, Sierra Leone. We thank Dr. Christopher Moxon for his critical edits of the manuscript. This work is supported by grants from the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) (U19AI110818 and R01AI114855 to the Broad Institute, P.C.S.), Henry M Jackson Foundation (W81XWH-18-2-0040 to P.C.S.), DARPA (D18AC00006 to the Broad Institute, P.C.S.), the Bill and Melinda Gates Foundation (OPP1192035 to Harvard University, P.C.S.), NIH-Fogarty (K01TW010853 to HTHCSPH, K.G.B.), and P.C.S. is supported by the Howard Hughes Medical Institute. Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

month = dec,

day = "1",

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

language = "English (US)",

volume = "11",

journal = "Nature communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

}

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.

N1 - Funding Information: Opinions, interpretations, conclusions, and recommendations are those of the authors and are not necessarily endorsed by the United States Army or the National Institute of Health. We thank the staff of the Joint West Africa Research Group, the Walter Reed Army Institute of Research, the Henry M. Jackson Foundation for the Advancement of Military Medicine, and the U.S. Embassy in Abuja, Nigeria, for their collaborative support and our colleagues at the Irrua Specialist Teaching Hospital, Nigeria, and Kenema Government Hospital, Sierra Leone. We thank Dr. Christopher Moxon for his critical edits of the manuscript. This work is supported by grants from the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) (U19AI110818 and R01AI114855 to the Broad Institute, P.C.S.), Henry M Jackson Foundation (W81XWH-18-2-0040 to P.C.S.), DARPA (D18AC00006 to the Broad Institute, P.C.S.), the Bill and Melinda Gates Foundation (OPP1192035 to Harvard University, P.C.S.), NIH-Fogarty (K01TW010853 to HTHCSPH, K.G.B.), and P.C.S. is supported by the Howard Hughes Medical Institute. Publisher Copyright: © 2020, The Author(s).

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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U2 - 10.1038/s41467-020-17994-9

DO - 10.1038/s41467-020-17994-9

M3 - Article

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AN - SCOPUS:85089533250

SN - 2041-1723

VL - 11

JO - Nature communications

JF - Nature communications

IS - 1

M1 - 4131

ER -

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

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