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Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med 2022; 28:1083-1094. [PMID: 35130561 PMCID: PMC9117129 DOI: 10.1038/s41591-022-01734-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/03/2022] [Indexed: 11/23/2022]
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.
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Affiliation(s)
- Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
| | - Meilin Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine Hua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Juliane Weller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Tien G Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew R Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Bennett M Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sri Gowtham Thakku
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Megan W Tse
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jared Kehe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jacqueline S Eversley
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Derek A Bielwaski
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Graham McGrath
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Braidt
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lydia A Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Brittany A Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Ewa King
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | - Richard C Huard
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | | | - Michael L Cleary
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | - Matthew W Keller
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marie K Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Christian T Happi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Springer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jacob E Lemieux
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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