Abstract
The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for ‘streamlined highlighting of infections to navigate epidemics, version 2’), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 932-943 |
| Number of pages | 12 |
| Journal | Nature Biomedical Engineering |
| Volume | 6 |
| Issue number | 8 |
| DOIs | |
| State | Published - Aug 2022 |
All Science Journal Classification (ASJC) codes
- Bioengineering
- Biotechnology
- Biomedical Engineering
- Medicine (miscellaneous)
- Computer Science Applications
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In: Nature Biomedical Engineering, Vol. 6, No. 8, 08.2022, p. 932-943.
Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants
AU - Arizti-Sanz, Jon
AU - Bradley, A’Doriann D.
AU - Zhang, Yibin B.
AU - Boehm, Chloe K.
AU - Freije, Catherine A.
AU - Grunberg, Michelle E.
AU - Kosoko-Thoroddsen, Tinna Solveig F.
AU - Welch, Nicole L.
AU - Pillai, Priya P.
AU - Mantena, Sreekar
AU - Kim, Gaeun
AU - Uwanibe, Jessica N.
AU - John, Oluwagboadurami G.
AU - Eromon, Philomena E.
AU - Kocher, Gregory
AU - Gross, Robin
AU - Lee, Justin S.
AU - Hensley, Lisa E.
AU - MacInnis, Bronwyn L.
AU - Johnson, Jeremy
AU - Springer, Michael
AU - Happi, Christian T.
AU - Sabeti, Pardis C.
AU - Myhrvold, Cameron
N1 - Funding Information: We thank the TIDE group at the Broad Institute for providing additional laboratory space to perform the work; all the researchers and laboratories who generously made SARS-CoV-2 sequencing data publicly available, to inform the design of our assay; H. Metsky for his contributions to the development of ADAPT, which guided the assay design; the Sabeti laboratory, notably S. Siddiqui, H. Metsky and E. Normandin for thoughtful discussions and reading of the manuscript; the personnel at the Rhode Island Department of Health for the samples they provided, in particular, E. King, Associate Director of Health, and R. C. Huard, Chief Clinical Laboratory Scientist, both at the Division of State Laboratories and Medical Examiner at Rhode Island Department of Health. Funding was provided by DARPA D18AC00006. This work was made possible by support from the Flu Lab and a cohort of generous donors through TED’s Audacious Project, including the ELMA Foundation, MacKenzie Scott, the Skoll Foundation and Open Philanthropy. J.A.-S. was supported by a fellowship from ‘la Caixa’ Foundation (ID 100010434, code LCF/BQ/AA18/11680098). C.M. was supported by start-up funds from Princeton University. For L.E.H., 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. M.S. was also supported by the National Institutes of Health (RO1 GM120122-01). P.C.S. was supported by the Howard Hughes Medical Institute, Merck KGaA Future Insight Prize and NIH (U01AI151812 and U54HG007480). 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. Funding Information: We thank the TIDE group at the Broad Institute for providing additional laboratory space to perform the work; all the researchers and laboratories who generously made SARS-CoV-2 sequencing data publicly available, to inform the design of our assay; H. Metsky for his contributions to the development of ADAPT, which guided the assay design; the Sabeti laboratory, notably S. Siddiqui, H. Metsky and E. Normandin for thoughtful discussions and reading of the manuscript; the personnel at the Rhode Island Department of Health for the samples they provided, in particular, E. King, Associate Director of Health, and R. C. Huard, Chief Clinical Laboratory Scientist, both at the Division of State Laboratories and Medical Examiner at Rhode Island Department of Health. Funding was provided by DARPA D18AC00006. This work was made possible by support from the Flu Lab and a cohort of generous donors through TED’s Audacious Project, including the ELMA Foundation, MacKenzie Scott, the Skoll Foundation and Open Philanthropy. J.A.-S. was supported by a fellowship from ‘la Caixa’ Foundation (ID 100010434, code LCF/BQ/AA18/11680098). C.M. was supported by start-up funds from Princeton University. For L.E.H., 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. M.S. was also supported by the National Institutes of Health (RO1 GM120122-01). P.C.S. was supported by the Howard Hughes Medical Institute, Merck KGaA Future Insight Prize and NIH (U01AI151812 and U54HG007480). 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: © 2022, The Author(s), under exclusive licence to Springer Nature Limited.
PY - 2022/8
Y1 - 2022/8
N2 - The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for ‘streamlined highlighting of infections to navigate epidemics, version 2’), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
AB - The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for ‘streamlined highlighting of infections to navigate epidemics, version 2’), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
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UR - http://www.scopus.com/inward/citedby.url?scp=85131086778&partnerID=8YFLogxK
U2 - 10.1038/s41551-022-00889-z
DO - 10.1038/s41551-022-00889-z
M3 - Article
C2 - 35637389
AN - SCOPUS:85131086778
SN - 2157-846X
VL - 6
SP - 932
EP - 943
JO - Nature Biomedical Engineering
JF - Nature Biomedical Engineering
IS - 8
ER -