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Panpradist N, Kline EC, Atkinson RG, Roller M, Wang Q, Hull IT, Kotnik JH, Oreskovic AK, Bennett C, Leon D, Lyon V, Gilligan-Steinberg SD, Han PD, Drain PK, Starita LM, Thompson MJ, Lutz BR. Harmony COVID-19: A ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection. Sci Adv 2021; 7:eabj1281. [PMID: 34910507 PMCID: PMC8673764 DOI: 10.1126/sciadv.abj1281] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/26/2021] [Indexed: 05/22/2023]
Abstract
RNA amplification tests sensitively detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but their complexity and cost are prohibitive for expanding coronavirus disease 2019 (COVID-19) testing. We developed “Harmony COVID-19,” a point-of-care test using inexpensive consumables, ready-to-use reagents, and a simple device. Our ready-to-use, multiplexed reverse transcription, loop-mediated isothermal amplification (RT-LAMP) can detect down to 0.38 SARS-CoV-2 RNA copies/μl and can report in 17 min for high–viral load samples (5000 copies/μl). Harmony detected 97 or 83% of contrived samples with ≥0.5 viral particles/μl in nasal matrix or saliva, respectively. Evaluation in clinical nasal specimens (n = 101) showed 100% detection of RNA extracted from specimens with ≥0.5 SARS-CoV-2 RNA copies/μl, with 100% specificity in specimens positive for other respiratory pathogens. Extraction-free analysis (n = 29) had 95% success in specimens with ≥1 RNA copies/μl. Usability testing performed first time by health care workers showed 95% accuracy.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Global Health for Women, Adolescents, and Children, School of Public Health, University of Washington, Seattle, WA, USA
| | - Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Robert G. Atkinson
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Michael Roller
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jack H. Kotnik
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Family Medicine, University of Washington, Seattle, WA, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Crissa Bennett
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Daniel Leon
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Victoria Lyon
- Department of Family Medicine, University of Washington, Seattle, WA, USA
| | | | - Peter D. Han
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paul K. Drain
- Departments of Global Health, Medicine, and Epidemiology, University of Washington, Seattle, WA, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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Panpradist N, Wang Q, Ruth PS, Kotnik JH, Oreskovic AK, Miller A, Stewart SWA, Vrana J, Han PD, Beck IA, Starita LM, Frenkel LM, Lutz BR. Simpler and faster Covid-19 testing: Strategies to streamline SARS-CoV-2 molecular assays. EBioMedicine 2021; 64:103236. [PMID: 33582488 PMCID: PMC7878117 DOI: 10.1016/j.ebiom.2021.103236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Detection of SARS-CoV-2 infections is important for treatment, isolation of infected and exposed individuals, and contact tracing. RT-qPCR is the "gold-standard" method to sensitively detect SARS-CoV-2 RNA, but most laboratory-developed RT-qPCR assays involve complex steps. Here, we aimed to simplify RT-qPCR assays by streamlining reaction setup, eliminating RNA extraction, and proposing reduced-cost detection workflows that avoid the need for expensive qPCR instruments. METHOD A low-cost RT-PCR based "kit" was developed for faster turnaround than the CDC developed protocol. We demonstrated three detection workflows: two that can be deployed in laboratories conducting assays of variable complexity, and one that could be simple enough for point-of-care. Analytical sensitivity was assessed using SARS-CoV-2 RNA spiked in simulated nasal matrix. Clinical performance was evaluated using contrived human nasal matrix (n = 41) and clinical nasal specimens collected from individuals with respiratory symptoms (n = 110). FINDING The analytical sensitivity of the lyophilised RT-PCR was 10 copies/reaction using purified SARS-CoV-2 RNA, and 20 copies/reaction when using direct lysate in simulated nasal matrix. Evaluation of assay performance on contrived human matrix showed 96.7-100% specificity and 100% sensitivity at ≥20 RNA copies. A head-to-head comparison with the standard CDC protocol on clinical specimens showed 83.8-94.6% sensitivity and 96.8-100% specificity. We found 3.6% indeterminate samples (undetected human control), lower than 8.1% with the standard protocol. INTERPRETATION This preliminary work should support laboratories or commercial entities to develop and expand access to Covid-19 testing. Software guidance development for this assay is ongoing to enable implementation in other settings. FUND: USA NIH R01AI140845 and Seattle Children's Research Institute.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, United States; Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, WA, United States
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Parker S Ruth
- Department of Bioengineering, University of Washington, Seattle, WA, United States; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, United States
| | - Jack H Kotnik
- Department of Bioengineering, University of Washington, Seattle, WA, United States; Department of Family Medicine, University of Washington, Seattle, WA, United States
| | - Amy K Oreskovic
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Abraham Miller
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Samuel W A Stewart
- Department of Bioengineering, University of Washington, Seattle, WA, United States; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Justin Vrana
- Department of Bioengineering, University of Washington, Seattle, WA, United States
| | - Peter D Han
- Department of Genome Sciences, Seattle, WA, United States; Brotman Baty Institute for Precision Medicine, Seattle, WA, United States
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Lea M Starita
- Department of Genome Sciences, Seattle, WA, United States; Brotman Baty Institute for Precision Medicine, Seattle, WA, United States
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States; Departments of Global Health, Medicine, Paediatrics, and Laboratory Medicine, University of Washington, Seattle, WA, United States.
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, United States; Brotman Baty Institute for Precision Medicine, Seattle, WA, United States.
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