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

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.; Carter, A.; Uwanibe, J.; Ajogbasile, F.; Olumade, T. J.; Odia, I.; Sandi, J. D.; Momoh, M.; Metsky, H. C.; Boehm, C. K.; Lin, A. E.; Kemball, M.; Park, D. J.; Grant, D. S.; Happi, C. T.; Branco, L.; Boisen, M.; Sullivan, B. M.; Amare, M.; Tiamiyu, A.; Parker, Z.; Iroezindu, M.; Modjarrad, K.; Myhrvold, C.; Garry, R. F.; Palacios, G.; Hensley, L. E.; Schaffner, S. F.; Colubri, A.; Sabeti, P. C.

doi:10.1101/2020.05.26.116442

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bioRxiv · 10.1101/2020.05.26.116442

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

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Abstract

Viral hemorrhagic fevers (VHFs) remain some of the most devastating human diseases, and recent outbreaks of Ebola virus disease (EVD) 1,2 and Lassa fever (LF) 3,4 highlight the urgent need for sensitive, field-deployable tests to diagnose them 5,6. 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. Our EBOV diagnostic detects both the L and NP genes, thereby eliminating the potential for false positive results caused by the rVSV{Delta}G-ZEBOV-GP live attenuated vaccine. Our two LASV diagnostics together capture 90% of known viral diversity and demonstrate that CRISPR-RNAs (crRNAs) can be effectively multiplexed to provide greater coverage of known viral diversity. We performed safety testing to demonstrate the efficacy of our HUDSON protocol in heat-inactivating and chemically treating VHF viruses before SHERLOCK testing, eliminating the need for an extraction. We developed a user-friendly field protocol and mobile application (HandLens) to report results, facilitating SHERLOCKs use in endemic regions. Finally, we successfully deployed our tests in Sierra Leone and Nigeria in response to recent outbreaks.

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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., Carter, A., Uwanibe, J., Ajogbasile, F., Olumade, T. J., Odia, I., Sandi, J. D., Momoh, M., Metsky, H. C., Boehm, C. K., Lin, A. E., Kemball, M., Park, D. J., Grant, D. S., Happi, C. T., Branco, L., Boisen, M., Sullivan, B. M., Amare, M., Tiamiyu, A., Parker, Z., Iroezindu, M., Modjarrad, K., Myhrvold, C., Garry, R. F., Palacios, G., Hensley, L. E., Schaffner, S. F., Colubri, A., Sabeti, P. C.. 2020-05-27. Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time. https://doi.org/10.1101/2020.05.26.116442

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