Abstract
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1083-1094 |
| Number of pages | 12 |
| Journal | Nature Medicine |
| Volume | 28 |
| Issue number | 5 |
| DOIs | |
| State | Published - May 2022 |
All Science Journal Classification (ASJC) codes
- Biochemistry, Genetics and Molecular Biology(all)
Access to Document
Other files and links
Fingerprint
Dive into the research topics of 'Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants'. Together they form a unique fingerprint.Cite this
- APA
- Author
- BIBTEX
- Harvard
- Standard
- RIS
- Vancouver
}
Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. / Welch, Nicole L.; Zhu, Meilin; Hua, Catherine et al.
In: Nature Medicine, Vol. 28, No. 5, 05.2022, p. 1083-1094.Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants
AU - Welch, Nicole L.
AU - Zhu, Meilin
AU - Hua, Catherine
AU - Weller, Juliane
AU - Mirhashemi, Marzieh Ezzaty
AU - Nguyen, Tien G.
AU - Mantena, Sreekar
AU - Bauer, Matthew R.
AU - Shaw, Bennett M.
AU - Ackerman, Cheri M.
AU - Thakku, Sri Gowtham
AU - Tse, Megan W.
AU - Kehe, Jared
AU - Uwera, Marie Martine
AU - Eversley, Jacqueline S.
AU - Bielwaski, Derek A.
AU - McGrath, Graham
AU - Braidt, Joseph
AU - Johnson, Jeremy
AU - Cerrato, Felecia
AU - Moreno, Gage K.
AU - Krasilnikova, Lydia A.
AU - Petros, Brittany A.
AU - Gionet, Gabrielle L.
AU - King, Ewa
AU - Huard, Richard C.
AU - Jalbert, Samantha K.
AU - Cleary, Michael L.
AU - Fitzgerald, Nicholas A.
AU - Gabriel, Stacey B.
AU - Gallagher, Glen R.
AU - Smole, Sandra C.
AU - Madoff, Lawrence C.
AU - Brown, Catherine M.
AU - Keller, Matthew W.
AU - Wilson, Malania M.
AU - Kirby, Marie K.
AU - Barnes, John R.
AU - Park, Daniel J.
AU - Siddle, Katherine J.
AU - Happi, Christian T.
AU - Hung, Deborah T.
AU - Springer, Michael
AU - MacInnis, Bronwyn L.
AU - Lemieux, Jacob E.
AU - Rosenberg, Eric
AU - Branda, John A.
AU - Blainey, Paul C.
AU - Sabeti, Pardis C.
AU - Myhrvold, Cameron
N1 - Funding Information: We thank the Blainey and Hung laboratories at the Broad Institute for providing additional laboratory space to perform the work; J. Arizti Sanz, Y. Zhang and A. Bradley for helping with guide design or sharing reagents; G. Adams, S. Dobbins, S. Slack, K. DeRuff and other members of the Sabeti laboratory COVID-19 sequencing team for providing patient samples; K. Carpenter-Azevedo from RIDOH for organizing and sending the Rhode Island patient samples; C. Tomkins-Tinch, C. Loreth and other Sabeti laboratory members for providing assistance with the NGS analysis on Terra; B. Zhou for helping provide the SARS-CoV-2 VOC seed stocks and patient samples; and H. Metsky, C. Freije, J. Arizti Sanz and S. Siddiqui for their thoughtful discussions and reading of the manuscript. We also acknowledge all members of the Massachusetts Department of Public Health, Broad Institute SARS-CoV-2 Genomics and Data Science Platforms and the Rhode Island Department of Public Health. Funding was provided by the Defense Advanced Research Projects Agency (no. D18AC00006). This work was made possible by support from the Flu laboratory and a cohort of generous donors through TED’s Audacious Project, including the ELMA Foundation, MacKenzie Scott, Skoll Foundation and Open Philanthropy. Funding for NGS was provided by the Centers for Disease Control and Prevention (CDC) COVID-19 baseline genomic surveillance contract sequencing (no. 75D30121C10501 to the Clinical Research Sequencing Platform), a CDC Broad Agency Announcement (no. 75D30120C09605 to B.L.M.) and the National Institute of Allergy and Infectious Diseases (nos. U19AI110818 and U01AI151812 to P.C.S.). M.Z. and M.W.T. were supported by the National Science Foundation Graduate Research Fellowship under grant no. 1745302. B.A.P. was supported by the National Institute of General Medical Sciences grant no. T32GM007753. P.C.S. was supported by the Howard Hughes Medical Institute and Merck KGaA Future Insight Prize. C.M. was supported by start-up funds from Princeton University. 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, Department of Homeland Security (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, Battelle National Biodefense Institute or National Biodefense Analysis and Countermeasures Center have any responsibility or liability for any use, misuse, inability to use or reliance on 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. The US Government retains and the publisher, by accepting the article for publication, acknowledges that the US Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US Government purposes. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the CDC. The use of trade names and commercial sources is for identification purposes only and does not imply endorsement. Funding Information: We thank the Blainey and Hung laboratories at the Broad Institute for providing additional laboratory space to perform the work; J. Arizti Sanz, Y. Zhang and A. Bradley for helping with guide design or sharing reagents; G. Adams, S. Dobbins, S. Slack, K. DeRuff and other members of the Sabeti laboratory COVID-19 sequencing team for providing patient samples; K. Carpenter-Azevedo from RIDOH for organizing and sending the Rhode Island patient samples; C. Tomkins-Tinch, C. Loreth and other Sabeti laboratory members for providing assistance with the NGS analysis on Terra; B. Zhou for helping provide the SARS-CoV-2 VOC seed stocks and patient samples; and H. Metsky, C. Freije, J. Arizti Sanz and S. Siddiqui for their thoughtful discussions and reading of the manuscript. We also acknowledge all members of the Massachusetts Department of Public Health, Broad Institute SARS-CoV-2 Genomics and Data Science Platforms and the Rhode Island Department of Public Health. Funding was provided by the Defense Advanced Research Projects Agency (no. D18AC00006). This work was made possible by support from the Flu laboratory and a cohort of generous donors through TED’s Audacious Project, including the ELMA Foundation, MacKenzie Scott, Skoll Foundation and Open Philanthropy. Funding for NGS was provided by the Centers for Disease Control and Prevention (CDC) COVID-19 baseline genomic surveillance contract sequencing (no. 75D30121C10501 to the Clinical Research Sequencing Platform), a CDC Broad Agency Announcement (no. 75D30120C09605 to B.L.M.) and the National Institute of Allergy and Infectious Diseases (nos. U19AI110818 and U01AI151812 to P.C.S.). M.Z. and M.W.T. were supported by the National Science Foundation Graduate Research Fellowship under grant no. 1745302. B.A.P. was supported by the National Institute of General Medical Sciences grant no. T32GM007753. P.C.S. was supported by the Howard Hughes Medical Institute and Merck KGaA Future Insight Prize. C.M. was supported by start-up funds from Princeton University. 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, Department of Homeland Security (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, Battelle National Biodefense Institute or National Biodefense Analysis and Countermeasures Center have any responsibility or liability for any use, misuse, inability to use or reliance on 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. The US Government retains and the publisher, by accepting the article for publication, acknowledges that the US Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for US Government purposes. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the CDC. The use of trade names and commercial sources is for identification purposes only and does not imply endorsement. Publisher Copyright: © 2022, The Author(s).
PY - 2022/5
Y1 - 2022/5
N2 - The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.
AB - The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.
UR - http://www.scopus.com/inward/record.url?scp=85126488987&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85126488987&partnerID=8YFLogxK
U2 - 10.1038/s41591-022-01734-1
DO - 10.1038/s41591-022-01734-1
M3 - Article
C2 - 35130561
AN - SCOPUS:85126488987
SN - 1078-8956
VL - 28
SP - 1083
EP - 1094
JO - Nature Medicine
JF - Nature Medicine
IS - 5
ER -