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

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 CerratoGage 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

Molecular Biology

Research output: Contribution to journal › Article › peer-review

95 Scopus citations

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	https://doi.org/10.1038/s41591-022-01734-1
State	Published - May 2022

All Science Journal Classification (ASJC) codes

Biochemistry, Genetics and Molecular Biology(all)

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10.1038/s41591-022-01734-1

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Welch, N. L., Zhu, M., Hua, C., Weller, J., Mirhashemi, M. E., Nguyen, T. G., Mantena, S., Bauer, M. R., Shaw, B. M., Ackerman, C. M., Thakku, S. G., Tse, M. W., Kehe, J., Uwera, M. M., Eversley, J. S., Bielwaski, D. A., McGrath, G., Braidt, J., Johnson, J., ... Myhrvold, C. (2022). Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nature Medicine, 28(5), 1083-1094. https://doi.org/10.1038/s41591-022-01734-1

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

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.",

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

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = may,

doi = "10.1038/s41591-022-01734-1",

language = "English (US)",

volume = "28",

pages = "1083--1094",

journal = "Nature Medicine",

issn = "1078-8956",

publisher = "Nature Publishing Group",

number = "5",

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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 2022, 'Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants', Nature Medicine, vol. 28, no. 5, pp. 1083-1094. https://doi.org/10.1038/s41591-022-01734-1

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

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.

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DO - 10.1038/s41591-022-01734-1

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JO - Nature Medicine

JF - Nature Medicine

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ER -

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

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