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Stahl EC, Gopez AR, Tsuchida CA, Fan VB, Moehle EA, Witkowsky LB, Hamilton JR, Lin-Shiao E, McElroy M, McDevitt SL, Ciling A, Tsui CK, Pestal K, Gildea HK, Keller A, Sylvain IA, Williams C, Hirsh A, Ehrenberg AJ, Kantor R, Metzger M, Nelson KL, Urnov FD, Ringeisen BR, Giannikopoulos P, Doudna JA. LuNER: Multiplexed SARS-CoV-2 detection in clinical swab and wastewater samples. PLoS One 2021; 16:e0258263. [PMID: 34758033 PMCID: PMC8580221 DOI: 10.1371/journal.pone.0258263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/22/2021] [Indexed: 01/03/2023] Open
Abstract
Clinical and surveillance testing for the SARS-CoV-2 virus relies overwhelmingly on RT-qPCR-based diagnostics, yet several popular assays require 2-3 separate reactions or rely on detection of a single viral target, which adds significant time, cost, and risk of false-negative results. Furthermore, multiplexed RT-qPCR tests that detect at least two SARS-CoV-2 genes in a single reaction are typically not affordable for large scale clinical surveillance or adaptable to multiple PCR machines and plate layouts. We developed a RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene, E gene, and human RNase P (LuNER) to address these shortcomings and meet the testing demands of a university campus and the local community. This cost-effective test is compatible with BioRad or Applied Biosystems qPCR machines, in 96 and 384-well formats, with or without sample pooling, and has a detection sensitivity suitable for both clinical reporting and wastewater surveillance efforts.
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Affiliation(s)
- Elizabeth C. Stahl
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Allan R. Gopez
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Connor A. Tsuchida
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Vinson B. Fan
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Erica A. Moehle
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Lea B. Witkowsky
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Jennifer R. Hamilton
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Enrique Lin-Shiao
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Matthew McElroy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Shana L. McDevitt
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Alison Ciling
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - C. Kimberly Tsui
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Kathleen Pestal
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Holly K. Gildea
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Amanda Keller
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Iman A. Sylvain
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Clara Williams
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Ariana Hirsh
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | | | - Rose Kantor
- University of California, Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Matthew Metzger
- University of California, Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Kara L. Nelson
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Fyodor D. Urnov
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Bradley R. Ringeisen
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Jennifer A. Doudna
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, CA, United States of America
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Agrawal S, Fanton A, Chandrasekaran SS, Charrez B, Escajeda AM, Son S, Mcintosh R, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. Rapid, point-of-care molecular diagnostics with Cas13. medRxiv 2021:2020.12.14.20247874. [PMID: 33354689 PMCID: PMC7755151 DOI: 10.1101/2020.12.14.20247874] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Rapid nucleic acid testing is a critical component of a robust infrastructure for increased disease surveillance. Here, we report a microfluidic platform for point-of-care, CRISPR-based molecular diagnostics. We first developed a nucleic acid test which pairs distinct mechanisms of DNA and RNA amplification optimized for high sensitivity and rapid kinetics, linked to Cas13 detection for specificity. We combined this workflow with an extraction-free sample lysis protocol using shelf-stable reagents that are widely available at low cost, and a multiplexed human gene control for calling negative test results. As a proof-of-concept, we demonstrate sensitivity down to 40 copies/μL of SARS-CoV-2 in unextracted saliva within 35 minutes, and validated the test on total RNA extracted from patient nasal swabs with a range of qPCR Ct values from 13-35. To enable sample-to-answer testing, we integrated this diagnostic reaction with a single-use, gravity-driven microfluidic cartridge followed by real-time fluorescent detection in a compact companion instrument. We envision this approach for Diagnostics with Coronavirus Enzymatic Reporting (DISCoVER) will incentivize frequent, fast, and easy testing.
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Affiliation(s)
- Shreeya Agrawal
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Sita S. Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Bérénice Charrez
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley—University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Neil A. Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R. Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Lukarska
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Dylan C. J. Smock
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J. Knott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Qi Dang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Eli Dugan
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Shin Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Tina Y. Liu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah A. Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- School of Public Health, University of California, Berkeley, CA, USA
| | - Liana F. Lareau
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A. Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Patrick D. Hsu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
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3
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Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, de León Derby MD, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim SE, Dugan EJ, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. Accelerated RNA detection using tandem CRISPR nucleases. medRxiv 2021:2021.03.19.21253328. [PMID: 33791736 PMCID: PMC8010768 DOI: 10.1101/2021.03.19.21253328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided recognition of RNA that triggers cleavage and release of a fluorescent reporter molecule1,2, but long reaction times hamper sensitivity and speed when applied to point-of-care testing. Here we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 RNA copies/microliter in 20 minutes. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that detected SARS-CoV-2 RNA from nasopharyngeal samples with PCR-derived Ct values up to 29 in microfluidic chips, using a compact imaging system. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables direct RNA detection in a format amenable to point-of-care infection diagnosis, as well as to a wide range of other diagnostic or research applications.
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Affiliation(s)
- Tina Y. Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J. Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, VIC 3800, Australia
| | - Dylan C. J. Smock
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - John J. Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Shrutee Jakhanwal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Shreeya Agrawal
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Neil A. Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R. Harris
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Emeric J. Charles
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brittney W. Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Parinaz Fozouni
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey Shu
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie I. Stephens
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chunyu Zhao
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Shin E. Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Katherine S. Pollard
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
| | | | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Liana F. Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Patrick D. Hsu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
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