Oil Immersed Lossless Total Analysis System for Integrated RNA Extraction and Detection of SARS-CoV-2

Overview

Journal Nat Commun

Specialty Biology

Date 2021 Jul 15

PMID 34262053

Citations 13

Authors

Duane S Juang

Terry D Juang

Dawn M Dudley

Christina M Newman

Molly A Accola

William M Rehrauer

Thomas C Friedrich

David H OConnor

David J Beebe

Affiliations

Soon will be listed here.

Abstract

The COVID-19 pandemic exposed difficulties in scaling current quantitative PCR (qPCR)-based diagnostic methodologies for large-scale infectious disease testing. Bottlenecks include lengthy multi-step processes for nucleic acid extraction followed by qPCR readouts, which require costly instrumentation and infrastructure, as well as reagent and plastic consumable shortages stemming from supply chain constraints. Here we report an Oil Immersed Lossless Total Analysis System (OIL-TAS), which integrates RNA extraction and detection onto a single device that is simple, rapid, cost effective, and requires minimal supplies and infrastructure to perform. We validated the performance of OIL-TAS using contrived SARS-CoV-2 viral particle samples and clinical nasopharyngeal swab samples. OIL-TAS showed a 93% positive predictive agreement (n = 57) and 100% negative predictive agreement (n = 10) with clinical SARS-CoV-2 qPCR assays in testing clinical samples, highlighting its potential to be a faster, cheaper, and easier-to-deploy alternative for infectious disease testing.

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References

Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N . Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000; 28(12):E63. PMC: 102748. DOI: 10.1093/nar/28.12.e63. View

Wang H, Wang Z, Dong Y, Chang R, Xu C, Yu X . Phase-adjusted estimation of the number of Coronavirus Disease 2019 cases in Wuhan, China. Cell Discov. 2020; 6:10. PMC: 7039910. DOI: 10.1038/s41421-020-0148-0. View

Li C, Yu J, Schehr J, Berry S, Leal T, Lang J . Exclusive Liquid Repellency: An Open Multi-Liquid-Phase Technology for Rare Cell Culture and Single-Cell Processing. ACS Appl Mater Interfaces. 2018; 10(20):17065-17070. PMC: 9703972. DOI: 10.1021/acsami.8b03627. View

Broughton J, Deng X, Yu G, Fasching C, Servellita V, Singh J . CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol. 2020; 38(7):870-874. PMC: 9107629. DOI: 10.1038/s41587-020-0513-4. View

Berry S, Pezzi H, Williams E, Loeb J, Guckenberger D, LaVanway A . Using Exclusion-Based Sample Preparation (ESP) to Reduce Viral Load Assay Cost. PLoS One. 2015; 10(12):e0143631. PMC: 4667969. DOI: 10.1371/journal.pone.0143631. View

Berry S, Pezzi H, LaVanway A, Guckenberger D, Anderson M, Beebe D . AirJump: Using Interfaces to Instantly Perform Simultaneous Extractions. ACS Appl Mater Interfaces. 2016; 8(24):15040-5. PMC: 5058634. DOI: 10.1021/acsami.6b02555. View

Yaffe H, Buxdorf K, Shapira I, Ein-Gedi S, Moyal-Ben Zvi M, Fridman E . LogSpin: a simple, economical and fast method for RNA isolation from infected or healthy plants and other eukaryotic tissues. BMC Res Notes. 2012; 5:45. PMC: 3282632. DOI: 10.1186/1756-0500-5-45. View

Casavant B, Guckenberger D, Berry S, Tokar J, Lang J, Beebe D . The VerIFAST: an integrated method for cell isolation and extracellular/intracellular staining. Lab Chip. 2012; 13(3):391-6. DOI: 10.1039/c2lc41136a. View

Oberacker P, Stepper P, Bond D, Hohn S, Focken J, Meyer V . Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation. PLoS Biol. 2019; 17(1):e3000107. PMC: 6343928. DOI: 10.1371/journal.pbio.3000107. View

10.

Curtis K, Morrison D, Rudolph D, Shankar A, Bloomfield L, Switzer W . A multiplexed RT-LAMP assay for detection of group M HIV-1 in plasma or whole blood. J Virol Methods. 2018; 255:91-97. DOI: 10.1016/j.jviromet.2018.02.012. View

11.

Berry S, Alarid E, Beebe D . One-step purification of nucleic acid for gene expression analysis via Immiscible Filtration Assisted by Surface Tension (IFAST). Lab Chip. 2011; 11(10):1747-53. PMC: 3244820. DOI: 10.1039/c1lc00004g. View

12.

Li C, Niles D, Juang D, Lang J, Beebe D . Automated System for Small-Population Single-Particle Processing Enabled by Exclusive Liquid Repellency. SLAS Technol. 2019; 24(6):535-542. PMC: 7521760. DOI: 10.1177/2472630319853219. View

13.

Berry S, Chin E, Jackson S, Strotman L, Goel M, Thompson N . Weak protein-protein interactions revealed by immiscible filtration assisted by surface tension. Anal Biochem. 2013; 447:133-40. PMC: 3897128. DOI: 10.1016/j.ab.2013.10.038. View

14.

Berry S, Strotman L, Kueck J, Alarid E, Beebe D . Purification of cell subpopulations via immiscible filtration assisted by surface tension (IFAST). Biomed Microdevices. 2011; 13(6):1033-42. PMC: 3314424. DOI: 10.1007/s10544-011-9573-z. View

15.

BOOM R, Sol C, Salimans M, Jansen C, van der Noordaa J . Rapid and simple method for purification of nucleic acids. J Clin Microbiol. 1990; 28(3):495-503. PMC: 269651. DOI: 10.1128/jcm.28.3.495-503.1990. View

16.

He H, Li R, Chen Y, Pan P, Tong W, Dong X . Integrated DNA and RNA extraction using magnetic beads from viral pathogens causing acute respiratory infections. Sci Rep. 2017; 7:45199. PMC: 5362898. DOI: 10.1038/srep45199. View

17.

Berry S, Regehr K, Casavant B, Beebe D . Automated operation of immiscible filtration assisted by surface tension (IFAST) arrays for streamlined analyte isolation. J Lab Autom. 2012; 18(3):206-11. PMC: 3633642. DOI: 10.1177/2211068212462023. View

18.

Rabe B, Cepko C . SARS-CoV-2 detection using isothermal amplification and a rapid, inexpensive protocol for sample inactivation and purification. Proc Natl Acad Sci U S A. 2020; 117(39):24450-24458. PMC: 7533677. DOI: 10.1073/pnas.2011221117. View

19.

Tanner N, Zhang Y, Evans Jr T . Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes. Biotechniques. 2015; 58(2):59-68. DOI: 10.2144/000114253. View

20.

Escobar M, Hunt J . A cost-effective RNA extraction technique from animal cells and tissue using silica columns. J Biol Methods. 2017; 4(2). PMC: 5503482. DOI: 10.14440/jbm.2017.184. View