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

TitleMultiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants.
Publication TypeJournal Article
Year of Publication2022
AuthorsWelch, 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
JournalNat Med
Volume28
Issue5
Pagination1083-1094
Date Published2022 May
ISSN1546-170X
KeywordsCOVID-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>

DOI10.1038/s41591-022-01734-1
Alternate JournalNat Med
PubMed ID35130561
PubMed Central IDPMC9117129
Grant ListT32 GM007753 / GM / NIGMS NIH HHS / United States
U19 AI110818 / AI / NIAID NIH HHS / United States
U01 AI151812 / AI / NIAID NIH HHS / United States
/ HHMI / Howard Hughes Medical Institute / United States