1. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants
- Author
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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, M-M, 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, 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, M-M, 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, and Myhrvold, C
- 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.
- Published
- 2022