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

Jon Arizti-Sanz; Catherine A. Freije; Alexandra C. Stanton; Brittany A. Petros; Chloe K. Boehm; Sameed Siddiqui; Bennett M. Shaw; Gordon Adams; Tinna Solveig F. Kosoko-Thoroddsen; Molly E. Kemball; Jessica N. Uwanibe; Fehintola V. Ajogbasile; Philomena E. Eromon; Robin Gross; Loni Wronka; Katie Caviness; Lisa E. Hensley; Nicholas H. Bergman; Bronwyn L. MacInnis; Christian T. Happi; Jacob E. Lemieux; Pardis C. Sabeti; Cameron Myhrvold

doi:10.1038/s41467-020-19097-x

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

Jon Arizti-Sanz, Catherine A. Freije, Alexandra C. Stanton, Brittany A. Petros, Chloe K. Boehm, Sameed Siddiqui, Bennett M. Shaw, Gordon Adams, Tinna Solveig F. Kosoko-Thoroddsen, Molly E. Kemball, Jessica N. Uwanibe, Fehintola V. Ajogbasile, Philomena E. Eromon, Robin Gross, Loni Wronka, Katie Caviness, Lisa E. Hensley, Nicholas H. Bergman, Bronwyn L. MacInnis, Christian T. HappiJacob E. Lemieux, Pardis C. Sabeti, Cameron Myhrvold

Molecular Biology

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

327 Scopus citations

Abstract

The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. SHINE’s 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-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

Original language	English (US)
Article number	5921
Journal	Nature communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-19097-x
State	Published - Dec 2020

All Science Journal Classification (ASJC) codes

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

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Arizti-Sanz, J., Freije, C. A., Stanton, A. C., Petros, B. A., Boehm, C. K., Siddiqui, S., Shaw, B. M., Adams, G., Kosoko-Thoroddsen, T. S. F., Kemball, M. E., Uwanibe, J. N., Ajogbasile, F. V., Eromon, P. E., Gross, R., Wronka, L., Caviness, K., Hensley, L. E., Bergman, N. H., MacInnis, B. L., ... Myhrvold, C. (2020). Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2. Nature communications, 11(1), Article 5921. https://doi.org/10.1038/s41467-020-19097-x

@article{85cd11744d0249b98117b000311ae531,

title = "Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2",

abstract = "The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. SHINE{\textquoteright}s 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-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.",

author = "Jon Arizti-Sanz and Freije, {Catherine A.} and Stanton, {Alexandra C.} and Petros, {Brittany A.} and Boehm, {Chloe K.} and Sameed Siddiqui and Shaw, {Bennett M.} and Gordon Adams and Kosoko-Thoroddsen, {Tinna Solveig F.} and Kemball, {Molly E.} and Uwanibe, {Jessica N.} and Ajogbasile, {Fehintola V.} and Eromon, {Philomena E.} and Robin Gross and Loni Wronka and Katie Caviness and Hensley, {Lisa E.} and Bergman, {Nicholas H.} and MacInnis, {Bronwyn L.} and Happi, {Christian T.} and Lemieux, {Jacob E.} and Sabeti, {Pardis C.} and Cameron Myhrvold",

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

year = "2020",

month = dec,

doi = "10.1038/s41467-020-19097-x",

language = "English (US)",

volume = "11",

journal = "Nature communications",

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Arizti-Sanz, J, Freije, CA, Stanton, AC, Petros, BA, Boehm, CK, Siddiqui, S, Shaw, BM, Adams, G, Kosoko-Thoroddsen, TSF, Kemball, ME, Uwanibe, JN, Ajogbasile, FV, Eromon, PE, Gross, R, Wronka, L, Caviness, K, Hensley, LE, Bergman, NH, MacInnis, BL, Happi, CT, Lemieux, JE, Sabeti, PC & Myhrvold, C 2020, 'Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2', Nature communications, vol. 11, no. 1, 5921. https://doi.org/10.1038/s41467-020-19097-x

TY - JOUR

T1 - Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2

AU - Arizti-Sanz, Jon

AU - Freije, Catherine A.

AU - Stanton, Alexandra C.

AU - Petros, Brittany A.

AU - Boehm, Chloe K.

AU - Siddiqui, Sameed

AU - Shaw, Bennett M.

AU - Adams, Gordon

AU - Kosoko-Thoroddsen, Tinna Solveig F.

AU - Kemball, Molly E.

AU - Uwanibe, Jessica N.

AU - Ajogbasile, Fehintola V.

AU - Eromon, Philomena E.

AU - Gross, Robin

AU - Wronka, Loni

AU - Caviness, Katie

AU - Hensley, Lisa E.

AU - Bergman, Nicholas H.

AU - MacInnis, Bronwyn L.

AU - Happi, Christian T.

AU - Lemieux, Jacob E.

AU - Sabeti, Pardis C.

AU - Myhrvold, Cameron

PY - 2020/12

Y1 - 2020/12

N2 - The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. SHINE’s 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-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

AB - The COVID-19 pandemic has highlighted that new diagnostic technologies are essential for controlling disease transmission. Here, we develop SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a sensitive and specific diagnostic tool that can detect SARS-CoV-2 RNA from unextracted samples. We identify the optimal conditions to allow RPA-based amplification and Cas13-based detection to occur in a single step, simplifying assay preparation and reducing run-time. We improve HUDSON to rapidly inactivate viruses in nasopharyngeal swabs and saliva in 10 min. SHINE’s 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-qPCR with a sample-to-answer time of 50 min. SHINE has the potential to be used outside of hospitals and clinical laboratories, greatly enhancing diagnostic capabilities.

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U2 - 10.1038/s41467-020-19097-x

DO - 10.1038/s41467-020-19097-x

M3 - Article

C2 - 33219225

AN - SCOPUS:85096325902

SN - 2041-1723

VL - 11

JO - Nature communications

JF - Nature communications

IS - 1

M1 - 5921

ER -

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

Abstract

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