Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants

Nicole L Welch; Meilin Zhu; Catherine Hua; Juliane Weller; Marzieh Ezzaty Mirhashemi; Tien G Nguyen; Sreekar Mantena; Matthew R Bauer; Bennett M Shaw; Cheri M Ackerman; Sri Gowtham Thakku; Megan W Tse; Jared Kehe; Marie-Martine Uwera; Jacqueline S Eversley; Derek A Bielwaski; Graham McGrath; Joseph Braidt; Jeremy Johnson; Felecia Cerrato; Gage K Moreno; Lydia A Krasilnikova; Brittany A Petros; Gabrielle L Gionet; Ewa King; Richard C Huard; Samantha K Jalbert; Michael L Cleary; Nicholas A Fitzgerald; Stacey B Gabriel; Glen R Gallagher; Sandra C Smole; Lawrence C Madoff; Catherine M Brown; Matthew W Keller; Malania M Wilson; Marie K Kirby; John R Barnes; Daniel J Park; Katherine J Siddle; Christian T Happi; Deborah T Hung; Michael Springer; Bronwyn L MacInnis; Jacob E Lemieux; Eric Rosenberg; John A Branda; Paul C Blainey; Pardis C Sabeti; Cameron Myhrvold

doi:10.1038/s41591-022-01734-1

Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants

Nat Med. 2022 May;28(5):1083-1094. doi: 10.1038/s41591-022-01734-1. Epub 2022 Feb 7.

Authors

Nicole L Welch^{1

2}, Meilin Zhu^{3

4}, Catherine Hua^{3

5}, Juliane Weller^{3

6}, Marzieh Ezzaty Mirhashemi³, Tien G Nguyen³, Sreekar Mantena³, Matthew R Bauer^{3

7}, Bennett M Shaw^{3

5}, Cheri M Ackerman^{3

4}, Sri Gowtham Thakku^{3

8}, Megan W Tse^{3

4}, Jared Kehe^{3

4}, Marie-Martine Uwera³, Jacqueline S Eversley⁵, Derek A Bielwaski⁵, Graham McGrath⁵, Joseph Braidt⁵, Jeremy Johnson³, Felecia Cerrato³, Gage K Moreno³, Lydia A Krasilnikova^{3

9}, Brittany A Petros^{3

8

10

11}, Gabrielle L Gionet³, Ewa King¹², Richard C Huard¹², Samantha K Jalbert¹¹, Michael L Cleary¹¹, Nicholas A Fitzgerald³, Stacey B Gabriel³, Glen R Gallagher¹³, Sandra C Smole¹³, Lawrence C Madoff¹³, Catherine M Brown¹³, Matthew W Keller¹⁴, Malania M Wilson¹⁴, Marie K Kirby¹⁴, John R Barnes¹⁴, Daniel J Park³, Katherine J Siddle^{3

9}, Christian T Happi^{3

15

16}, Deborah T Hung^{3

17}, Michael Springer^{3

11}, Bronwyn L MacInnis^{3

18}, Jacob E Lemieux^{3

5}, Eric Rosenberg^{5

19}, John A Branda¹⁹, Paul C Blainey^{3

4

20}, Pardis C Sabeti^{21

22

23

24

25}, Cameron Myhrvold²⁶

Affiliations

¹ Broad Institute of MIT and Harvard, Cambridge, MA, USA. nicole_welch@g.harvard.edu.
² Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA. nicole_welch@g.harvard.edu.
³ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁴ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵ Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
⁶ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
⁷ Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.
⁸ Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA.
⁹ Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
¹⁰ Harvard/Massachusetts Institute of Technology MD-PhD Program, Harvard Medical School, Boston, MA, USA.
¹¹ Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
¹² State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA.
¹³ Massachusetts Department of Public Health, Boston, MA, USA.
¹⁴ Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
¹⁵ African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria.
¹⁶ Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Nigeria.
¹⁷ Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
¹⁸ Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
¹⁹ Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
²⁰ Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA.
²¹ Broad Institute of MIT and Harvard, Cambridge, MA, USA. pardis@broadinstitute.org.
²² Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA. pardis@broadinstitute.org.
²³ Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA. pardis@broadinstitute.org.
²⁴ Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA. pardis@broadinstitute.org.
²⁵ Howard Hughes Medical Institute, Chevy Chase, MD, USA. pardis@broadinstitute.org.
²⁶ Department of Molecular Biology, Princeton University, Princeton, NJ, USA. cmyhrvol@princeton.edu.

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.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, U.S. Gov't, P.H.S.
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

COVID-19* / diagnosis
Humans
Influenza, Human*
Microfluidics
SARS-CoV-2 / genetics

Supplementary concepts

SARS-CoV-2 variants

Abstract

Publication types

MeSH terms

Supplementary concepts

Grants and funding