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
N1 - Funding Information:
We would like to thank E. Rosenberg for kindly providing patient samples used in this study; the Harvard Medical School Systems Biology Department, Harvard University Northwest Labs, and A. Viel for providing additional laboratory space to perform the work; those researchers and laboratories who generously made SARS-CoV-2 sequencing data publicly available to aid in our assay design; members of the Sabeti laboratory—N. Welch, E. Normandin, K. DeRuff, K. Lagerborg, M. Bauer, M. Rudy, K. Siddle, A. Lin, and A. Gladden-Young—for assisting with patient sample collection and processing; H. Metsky, for his contributions to the assay design; M. Springer, the Springer laboratory, and the Sabeti laboratory, notably H. Metsky, A. Lin, and N. Welch for their thoughtful discussions and reading of the manuscript. Funding was provided by DARPA D18AC00006 and the Open Philanthropy Project. J.A.-S. is supported by a fellowship from “la Caixa” Foundation (ID 100010434, code LCF/BQ/AA18/11680098). B.A.P. is supported by the National Institute of General Medical Sciences grant T32GM007753. For L.W., K.C., and N.H. B., this work was funded under Agreement No. HSHQDC-15-C-00064 awarded to Battelle National Biodefense Institute (BNBI) by the Department of Homeland Security (DHS) Science and Technology (S&T) Directorate for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center. The views, opinions, conclusions, and/or findings expressed should not be interpreted as representing the official views or policies, either expressed or implied of the Department of Defense, US government, National Institute of General Medical Sciences, DHS, or the National Institutes of Health. The DHS does not endorse any products or commercial services mentioned in this presentation. In no event shall the DHS, BNBI or NBACC have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. In addition, no warranty of fitness for a particular purpose, merchantability, accuracy or adequacy is provided regarding the contents of this document.Notice: This manuscript has been authored by Battelle National Biodefense Institute, LLC under Contract No. HSHQDC-15-C-00064 with the U.S. Department of Homeland Security. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.
Publisher Copyright:
© 2020, The Author(s).
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 -