Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2

Arizti-Sanz, J.; Freije, C. A.; Stanton, A. C.; Boehm, C. K.; Petros, B. A.; Siddiqui, S.; Shaw, B. M.; Adams, G.; Kosoko-Thoroddsen, T.-S. F.; Kemball, M. E.; Gross, R.; Wronka, L.; Caviness, K.; Hensley, L. E.; Bergman, N. H.; MacInnis, B. L.; Lemieux, J. E.; Sabeti, P. C.; Myhrvold, C.

doi:10.1101/2020.05.28.119131

bioRxiv · 10.1101/2020.05.28.119131

Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2

Arizti-Sanz, J.·Freije, C. A.·Stanton, A. C.·Boehm, C. K.·Petros, B. A.·Siddiqui, S.·Shaw, B. M.·Adams, G.·Kosoko-Thoroddsen, T.-S. F.·Kemball, M. E.·Gross, R.·Wronka, L.·Caviness, K.·Hensley, L. E.·Bergman, N. H.·MacInnis, B. L.·Lemieux, J. E.·Sabeti, P. C.·Myhrvold, C.

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Abstract

The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (SHERLOCK and HUDSON Integration to Navigate Epidemics), a sensitive and specific integrated diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We combine the steps of SHERLOCK into a single-step reaction and optimize HUDSON to accelerate viral inactivation in nasopharyngeal swabs and saliva. SHINEs results can be visualized with an in-tube fluorescent readout -- reducing contamination risk as amplification reaction tubes remain sealed -- and interpreted by a companion smartphone application. We validate SHINE on 50 nasopharyngeal patient samples, demonstrating 90% sensitivity and 100% specificity compared to RT-PCR with a sample-to-answer time of 50 minutes. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

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Arizti-Sanz, J., Freije, C. A., Stanton, A. C., Boehm, C. K., Petros, B. A., Siddiqui, S., Shaw, B. M., Adams, G., Kosoko-Thoroddsen, T.-S. F., Kemball, M. E., Gross, R., Wronka, L., Caviness, K., Hensley, L. E., Bergman, N. H., MacInnis, B. L., Lemieux, J. E., Sabeti, P. C., Myhrvold, C.. 2020-05-28. Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2. https://doi.org/10.1101/2020.05.28.119131

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