Title | Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. |
Publication Type | Journal Article |
Year of Publication | 2022 |
Authors | Welch, NL, Zhu, M, Hua, C, Weller, J, Mirhashemi, MEzzaty, Nguyen, TG, Mantena, S, Bauer, MR, Shaw, BM, Ackerman, CM, Thakku, SGowtham, 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 |
Journal | Nat Med |
Volume | 28 |
Issue | 5 |
Pagination | 1083-1094 |
Date Published | 2022 May |
ISSN | 1546-170X |
Keywords | COVID-19, Humans, Influenza, Human, Microfluidics, SARS-CoV-2 |
Abstract | <p>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.</p> |
DOI | 10.1038/s41591-022-01734-1 |
Alternate Journal | Nat Med |
PubMed ID | 35130561 |
PubMed Central ID | PMC9117129 |
Grant List | T32 GM007753 / GM / NIGMS NIH HHS / United States U01 AI151812 / AI / NIAID NIH HHS / United States U19 AI110818 / AI / NIAID NIH HHS / United States / HHMI / Howard Hughes Medical Institute / United States |