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Wang Q, Kline EC, Gilligan-Steinberg SD, Lai JJ, Hull IT, Olanrewaju AO, Panpradist N, Lutz BR. Sensitive Pathogen Detection and Drug Resistance Characterization Using Pathogen-Derived Enzyme Activity Amplified by LAMP or CRISPR-Cas. medRxiv 2024:2024.03.29.24305085. [PMID: 38633802 PMCID: PMC11023665 DOI: 10.1101/2024.03.29.24305085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Pathogens encapsulate or encode their own suite of enzymes to facilitate replication in the host. The pathogen-derived enzymes possess specialized activities that are essential for pathogen replication and have naturally been candidates for drug targets. Phenotypic assays detecting the activities of pathogen-derived enzymes and characterizing their inhibition under drugs offer an opportunity for pathogen detection, drug resistance testing for individual patients, and as a research tool for new drug development. Here, we used HIV as an example to develop assays targeting the reverse transcriptase (RT) enzyme encapsulated in HIV for sensitive detection and phenotypic characterization, with the potential for point-of-care (POC) applications. Specifically, we targeted the complementary (cDNA) generation activity of the HIV RT enzyme by adding engineered RNA as substrates for HIV RT enzyme to generate cDNA products, followed by cDNA amplification and detection facilitated by loop-mediated isothermal amplification (LAMP) or CRISPR-Cas systems. To guide the assay design, we first used qPCR to characterize the cDNA generation activity of HIV RT enzyme. In the LAMP-mediated Product-Amplified RT activity assay (LamPART), the cDNA generation and LAMP amplification were combined into one pot with novel assay designs. When coupled with direct immunocapture of HIV RT enzyme for sample preparation and endpoint lateral flow assays for detection, LamPART detected as few as 20 copies of HIV RT enzyme spiked into 25μL plasma (fingerstick volume), equivalent to a single virion. In the Cas-mediated Product-Amplified RT activity assay (CasPART), we tailored the substrate design to achieve a LoD of 2e4 copies (1.67fM) of HIV RT enzyme. Furthermore, with its phenotypic characterization capability, CasPART was used to characterize the inhibition of HIV RT enzyme under antiretroviral drugs and differentiate between wild-type and mutant HIV RT enzyme for potential phenotypic drug resistance testing. Moreover, the CasPART assay can be readily adapted to target the activity of other pathogen-derived enzymes. As a proof-of-concept, we successfully adapted CasPART to detect HIV integrase with a sensitivity of 83nM. We anticipate the developed approach of detecting enzyme activity with product amplification has the potential for a wide range of pathogen detection and phenotypic characterization.
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Affiliation(s)
- Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Materials Science and Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Ayokunle O. Olanrewaju
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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Wang Q, Panpradist N, Kotnik JH, Willson RC, Kourentzi K, Chau ZL, Liu JK, Lutz BR, Lai JJ. A simple agglutination system for rapid antigen detection from large sample volumes with enhanced sensitivity. Anal Chim Acta 2023; 1277:341674. [PMID: 37604625 PMCID: PMC10777812 DOI: 10.1016/j.aca.2023.341674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/14/2023] [Accepted: 07/29/2023] [Indexed: 08/23/2023]
Abstract
Lateral flow assays (LFAs) provide a simple and quick option for diagnosis and are widely adopted for point-of-care or at-home tests. However, their sensitivity is often limited. Most LFAs only allow 50 μL samples while various sample types such as saliva could be collected in much larger volumes. Adapting LFAs to accommodate larger sample volumes can improve assay sensitivity by increasing the number of target analytes available for detection. Here, a simple agglutination system comprising biotinylated antibody (Ab) and streptavidin (SA) is presented. The Ab and SA agglutinate into large aggregates due to multiple biotins per Ab and multiple biotin binding sites per SA. Dynamic light scattering (DLS) measurements showed that the agglutinated aggregate could reach a diameter of over 0.5 μm and over 1.5 μm using poly-SA. Through both experiments and Monte Carlo modeling, we found that high valency and equivalent concentrations of the two aggregating components were critical for successful agglutination. The simple agglutination system enables antigen capture from large sample volumes with biotinylated Ab and a swift transition into aggregates that can be collected via filtration. Combining the agglutination system with conventional immunoassays, an agglutination assay is proposed that enables antigen detection from large sample volumes using an in-house 3D-printed device. As a proof-of-concept, we developed an agglutination assay targeting SARS-CoV-2 nucleocapsid antigen for COVID-19 diagnosis from saliva. The assay showed a 10-fold sensitivity enhancement when increasing sample volume from 50 μL to 2 mL, with a final limit of detection (LoD) of 10 pg mL-1 (∼250 fM). The assay was further validated in negative saliva spiked with gamma-irradiated SARS-CoV-2 and showed an LoD of 250 genome copies per μL. The proposed agglutination assay can be easily developed from existing LFAs to facilitate the processing of large sample volumes for improved sensitivity.
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Affiliation(s)
- Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA, 98195-5061, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, 98195-5061, USA
| | - Jack Henry Kotnik
- Department of Bioengineering, University of Washington, Seattle, WA, 98195-5061, USA
| | - Richard C Willson
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, 77204, USA
| | - Zoe L Chau
- Department of Bioengineering, University of Washington, Seattle, WA, 98195-5061, USA
| | - Joanne K Liu
- Department of Bioengineering, University of Washington, Seattle, WA, 98195-5061, USA
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, 98195-5061, USA.
| | - James J Lai
- Department of Bioengineering, University of Washington, Seattle, WA, 98195-5061, USA; Department of Materials Science and Engineering, National Taiwan University of Science and Technology, Taipei, 106335, Taiwan.
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Iribarren SJ, Milligan H, Chirico C, Goodwin K, Schnall R, Telles H, Iannizzotto A, Sanjurjo M, Lutz BR, Pike K, Rubinstein F, Rhodehamel M, Leon D, Keyes J, Demiris G. Patient-centered mobile tuberculosis treatment support tools (TB-TSTs) to improve treatment adherence: A pilot randomized controlled trial exploring feasibility, acceptability and refinement needs. Lancet Reg Health Am 2022; 13:100291. [PMID: 36061038 PMCID: PMC9426680 DOI: 10.1016/j.lana.2022.100291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Background Digital adherence technologies hold promise to improve patient-centered tuberculosis (TB) monitoring, yet few studies have incorporated direct adherence monitoring or assessed patients' experiences with these technologies. We explored acceptability, feasibility, and refinement needs of the TB Treatment Support Tools (TB-TSTs) intervention linking a mobile app, a urine drug metabolite test, and interactive communication with a treatment supporter. Methods This pilot study was a parallel-designed single-center randomized controlled trial with exit interviews. Newly diagnosed TB patients were randomized 1:1 using a treatment allocation button in the REDCap software preloaded with a random allocation sequence to usual care or usual care plus the TB-TSTs intervention from a respiratory medicine hospital in the province of Buenos Aires, Argentina and followed for 6-months. Due to the nature of the intervention, blinding to the group allocation could not be achieved for the recruiter or patients. The treatment outcome data extractor was blinded to the group allocation of the participants. Intervention participants used the app to report self-administering medication, potential side effects, submit photos of the urine test, and interact with a treatment supporter. Outcomes were feasibility, acceptability, and treatment outcomes. Findings Forty-two patients were enrolled and evenly assigned to each group. Intervention participants submitted 147·2±58 (mean, SD) medication self-administration and 144·5±55 side effect reports out of 180 and 47.5±38·4 photos of the urine test out of 77. Treatment success for usual care was 81% [17/21] and 95% [20/21] for the TB-TSTs intervention. Thirty-three themes were identified within the main categories of motivation, what worked, issues experienced, and recommendations. Participants (n=12) rated it as 'easy to use' (4.57/5), 'would highly recommend to others' (4·43/5) and reported that access to the treatment support was a critical component. Recommendations included adding an alarm, appointment reminders, and off-line functionality. Interpretation Findings suggest that the TB-TSTs intervention was feasible and acceptable and further refinement and testing is warranted. Funding National Institute of Health K23NR017210.
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Affiliation(s)
- Sarah J Iribarren
- Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, WA, USA
| | - Hannah Milligan
- Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, WA, USA
| | - Cristina Chirico
- Tuberculosis Control Program of the 5 Health Region, Ministry of Health of the Province of Buenos Aires, Hospital Cetrángolo, Buenos Aires, Argentina
| | - Kyle Goodwin
- Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, WA, USA
| | - Rebecca Schnall
- Columbia University School of Nursing, New York City, NY, USA
| | - Hugo Telles
- Tuberculosis Control Program of the 5 Health Region, Ministry of Health of the Province of Buenos Aires, Hospital Cetrángolo, Buenos Aires, Argentina
| | - Alejandra Iannizzotto
- Tuberculosis Control Program of the 5 Health Region, Ministry of Health of the Province of Buenos Aires, Hospital Cetrángolo, Buenos Aires, Argentina
| | - Myrian Sanjurjo
- Hospital del Tórax Dr. Antonio A. Cetrángolo, Provincia de Buenos Aires, Argentina
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Kenneth Pike
- Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, WA, USA
| | - Fernando Rubinstein
- Institute of Clinical Effectiveness and Health Policy (IECS), Buenos Aires, Argentina
| | - Marcus Rhodehamel
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Daniel Leon
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jesse Keyes
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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Kline EC, Panpradist N, Hull IT, Wang Q, Oreskovic AK, Han PD, Starita LM, Lutz BR. Multiplex Target-Redundant RT-LAMP for Robust Detection of SARS-CoV-2 Using Fluorescent Universal Displacement Probes. Microbiol Spectr 2022; 10:e0158321. [PMID: 35708340 PMCID: PMC9430505 DOI: 10.1128/spectrum.01583-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 09/20/2021] [Accepted: 05/06/2022] [Indexed: 11/20/2022] Open
Abstract
The increasing prevalence of variant lineages during the COVID-19 pandemic has the potential to disrupt molecular diagnostics due to mismatches between primers and variant templates. Point-of-care molecular diagnostics, which often lack the complete functionality of their high-throughput laboratory counterparts, are particularly susceptible to this type of disruption, which can result in false-negative results. To address this challenge, we have developed a robust Loop Mediated Isothermal Amplification assay with single tube multiplexed multitarget redundancy and an internal amplification control. A convenient and cost-effective target-specific fluorescence detection system allows amplifications to be grouped by signal using adaptable probes for pooled reporting of SARS-CoV-2 target amplifications or differentiation of the Internal Amplification Control. Over the course of the pandemic, primer coverage of viral lineages by the three redundant sub-assays has varied from assay to assay as they have diverged from the Wuhan-Hu-1 isolate sequence, but aggregate coverage has remained high for all variant sequences analyzed, with a minimum of 97.4% (Variant of Interest: Eta). In three instances (Delta, Gamma, Eta), a high-frequency mismatch with one of the three sub-assays was observed, but overall coverage remained high due to multitarget redundancy. When challenged with extracted human samples the multiplex assay showed 87% or better sensitivity (of 30 positive samples), with 100% sensitivity for samples containing greater than 30 copies of viral RNA per reaction (of 21 positive samples), and 100% specificity (of 60 negative samples). These results are further evidence that conventional laboratory methodologies can be leveraged at the point of care for robust performance and diagnostic stability over time. IMPORTANCE The COVID-19 pandemic has had tremendous impact, and the ability to perform molecular diagnostics in resource limited settings has emerged as a key resource for mitigating spread of the disease. One challenge in COVID-19 diagnosis, as well as other viruses, is ongoing mutation that can allow viruses to evade detection by diagnostic tests. We developed a test that detects multiple parts of the virus genome in a single test to reduce the chance of missing a virus due to mutation, and it is designed to be simpler and faster than typical laboratory tests while maintaining high sensitivity. This capability is enabled by a novel fluorescent probe technology that works with a simple constant temperature reaction condition.
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Affiliation(s)
- Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health for Women Adolescents and Children, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Peter D. Han
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
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5
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Yang LF, Kacherovsky N, Panpradist N, Wan R, Liang J, Zhang B, Salipante SJ, Lutz BR, Pun SH. Aptamer Sandwich Lateral Flow Assay (AptaFlow) for Antibody-Free SARS-CoV-2 Detection. Anal Chem 2022; 94:7278-7285. [PMID: 35532905 PMCID: PMC9112978 DOI: 10.1021/acs.analchem.2c00554] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 02/01/2022] [Accepted: 04/10/2022] [Indexed: 12/17/2022]
Abstract
The COVID-19 pandemic is among the greatest health and socioeconomic crises in recent history. Although COVID-19 vaccines are being distributed, there remains a need for rapid testing to limit viral spread from infected individuals. We previously identified the SARS-CoV-2 spike protein N-terminal domain (NTD) binding DNA aptamer 1 (SNAP1) for detection of SARS-CoV-2 virus by aptamer-antibody sandwich enzyme-linked immunoassay (ELISA) and lateral flow assay (LFA). In this work, we identify a new aptamer that also binds at the NTD, named SARS-CoV-2 spike protein NTD-binding DNA aptamer 4 (SNAP4). SNAP4 binds with high affinity (<30 nM) for the SARS-CoV-2 spike protein, a 2-fold improvement over SNAP1. Furthermore, we utilized both SNAP1 and SNAP4 in an aptamer sandwich LFA (AptaFlow), which detected SARS-CoV-2 UV-inactivated virus at concentrations as low as 106 copies/mL. AptaFlow costs <$1 per test to produce, provides results in <1 h, and detects SARS-CoV-2 at concentrations that indicate higher viral loads and a high probability of contagious transmission. AptaFlow is a potential approach for a low-cost, convenient antigen test to aid the control of the COVID-19 pandemic.
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Affiliation(s)
- Lucy F. Yang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Nuttada Panpradist
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Ruixuan Wan
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Joey Liang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Bo Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Stephen J. Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195
| | - Barry R. Lutz
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
| | - Suzie H. Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195
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6
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Hull IT, Kline EC, Gulati GK, Kotnik JH, Panpradist N, Shah KG, Wang Q, Frenkel L, Lai J, Stekler J, Lutz BR. Addition to "Isothermal Amplification with a Target-Mimicking Internal Control and Quantitative Lateral Flow Readout for Rapid HIV Viral Load Testing in Low-Resource Settings". Anal Chem 2022; 94:6071. [PMID: 35380786 DOI: 10.1021/acs.analchem.2c01256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Vrana JD, Panpradist N, Higa N, Ko D, Ruth P, Kanthula R, Lai JJ, Yang Y, Sakr SR, Chohan B, Chung MH, Frenkel LM, Lutz BR, Klavins E, Beck IA. Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya. PLOS Glob Public Health 2022. [PMID: 36962187 DOI: 10.1101/2021.05.06.21256654v1.full.pdf+html] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Usability is an overlooked aspect of implementing lab-based assays, particularly novel assays in low-resource-settings. Esoteric instructions can lead to irreproducible test results and patient harm. To address these issues, we developed a software application based on "Aquarium", a laboratory-operating system run on a computer tablet that provides step-by-step digital interactive instructions, protocol management, and sample tracking. Aquarium was paired with a near point-of-care HIV drug resistance test, "OLA-Simple", that detects mutations associated with virologic failure. In this observational study we evaluated the performance of Aquarium in guiding untrained users through the multi-step laboratory protocol with little supervision. To evaluate the training by Aquarium software we conducted a feasibility study in a laboratory at Coptic Hope Center in Nairobi, Kenya. Twelve volunteers who were unfamiliar with the kit performed the test on blinded samples (2 blood specimens; 5 codons/sample). Steps guided by Aquarium included: CD4+ T-Cell separation, PCR, ligation, detection, and interpretation of test results. Participants filled out a short survey regarding their demographics and experience with the software and kit. None of the laboratory technicians had prior experience performing CD4+ separation and 7/12 had no experience performing laboratory-based molecular assays. 12/12 isolated CD4+ T cells from whole blood with yields comparable to isolations performed by trained personnel. The OLA-Simple workflow was completed by all, with genotyping results interpreted correctly by unaided-eye in 108/120 (90%) and by software in 116/120 (97%) of codons analyzed. In the surveys, participants favorably assessed the use of software guidance. The Aquarium digital instructions enabled first-time users in Kenya to complete the OLA-simple kit workflow with minimal training. Aquarium could increase the accessibility of laboratory assays in low-resource-settings and potentially standardize implementation of clinical laboratory tests.
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Affiliation(s)
- Justin D Vrana
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Nikki Higa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Parker Ruth
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ruth Kanthula
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - James J Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Yaoyu Yang
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Samar R Sakr
- Coptic Hope Center for Infectious Diseases, Nairobi, Kenya
| | - Bhavna Chohan
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michael H Chung
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
- Departments of Global Health, Medicine, Pediatrics, and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Eric Klavins
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
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8
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Vrana JD, Panpradist N, Higa N, Ko D, Ruth P, Kanthula R, Lai JJ, Yang Y, Sakr SR, Chohan B, Chung MH, Frenkel LM, Lutz BR, Klavins E, Beck IA. Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya. PLOS Glob Public Health 2022; 2:e0000185. [PMID: 36962187 PMCID: PMC10021139 DOI: 10.1371/journal.pgph.0000185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/09/2022] [Indexed: 04/24/2023]
Abstract
Usability is an overlooked aspect of implementing lab-based assays, particularly novel assays in low-resource-settings. Esoteric instructions can lead to irreproducible test results and patient harm. To address these issues, we developed a software application based on "Aquarium", a laboratory-operating system run on a computer tablet that provides step-by-step digital interactive instructions, protocol management, and sample tracking. Aquarium was paired with a near point-of-care HIV drug resistance test, "OLA-Simple", that detects mutations associated with virologic failure. In this observational study we evaluated the performance of Aquarium in guiding untrained users through the multi-step laboratory protocol with little supervision. To evaluate the training by Aquarium software we conducted a feasibility study in a laboratory at Coptic Hope Center in Nairobi, Kenya. Twelve volunteers who were unfamiliar with the kit performed the test on blinded samples (2 blood specimens; 5 codons/sample). Steps guided by Aquarium included: CD4+ T-Cell separation, PCR, ligation, detection, and interpretation of test results. Participants filled out a short survey regarding their demographics and experience with the software and kit. None of the laboratory technicians had prior experience performing CD4+ separation and 7/12 had no experience performing laboratory-based molecular assays. 12/12 isolated CD4+ T cells from whole blood with yields comparable to isolations performed by trained personnel. The OLA-Simple workflow was completed by all, with genotyping results interpreted correctly by unaided-eye in 108/120 (90%) and by software in 116/120 (97%) of codons analyzed. In the surveys, participants favorably assessed the use of software guidance. The Aquarium digital instructions enabled first-time users in Kenya to complete the OLA-simple kit workflow with minimal training. Aquarium could increase the accessibility of laboratory assays in low-resource-settings and potentially standardize implementation of clinical laboratory tests.
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Affiliation(s)
- Justin D. Vrana
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Nikki Higa
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Parker Ruth
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, Washington, United States of America
| | - Ruth Kanthula
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, United States of America
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Yaoyu Yang
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Samar R. Sakr
- Coptic Hope Center for Infectious Diseases, Nairobi, Kenya
| | - Bhavna Chohan
- Center for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michael H. Chung
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Departments of Global Health, Medicine, Pediatrics, and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Eric Klavins
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
- * E-mail: (EK); (IAB)
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- * E-mail: (EK); (IAB)
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9
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Gulati GK, Panpradist N, Stewart SWA, Beck IA, Boyce C, Oreskovic AK, García-Morales C, Avila-Ríos S, Han PD, Reyes-Terán G, Starita LM, Frenkel LM, Lutz BR, Lai JJ. Simultaneous monitoring of HIV viral load and screening of SARS-CoV-2 employing a low-cost RT-qPCR test workflow. Analyst 2022; 147:3315-3327. [PMID: 35762367 PMCID: PMC10143869 DOI: 10.1039/d2an00405d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This new workflow enables co-extraction of HIV and SARS-CoV2 RNAs from clinical pooled plasma/nasal secretion samples that allows sensitive detection of SARS-CoV-2 and HIV infections in the patients-living with HIV.
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Affiliation(s)
- Gaurav K. Gulati
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, USA
| | - Samuel W. A. Stewart
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ceejay Boyce
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Santiago Avila-Ríos
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Peter D. Han
- Department of Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Gustavo Reyes-Terán
- Coordination of the Mexican National Institutes of Health and High Specialty Hospitals, Mexico City, Mexico
| | - Lea M. Starita
- Department of Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Departments of Medicine, Pediatrics, Laboratory Medicine and Pathology, Global Health and Medicine, University of Washington, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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10
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Hull IT, Kline EC, Gulati GK, Kotnik JH, Panpradist N, Shah KG, Wang Q, Frenkel L, Lai J, Stekler J, Lutz BR. Isothermal Amplification with a Target-Mimicking Internal Control and Quantitative Lateral Flow Readout for Rapid HIV Viral Load Testing in Low-Resource Settings. Anal Chem 2021; 94:1011-1021. [PMID: 34920665 DOI: 10.1021/acs.analchem.1c03960] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Point-of-care diagnostics often use isothermal nucleic acid amplification for qualitative detection of pathogens in low-resource healthcare settings but lack sufficient precision for quantitative applications such as HIV viral load monitoring. Although viral load (VL) monitoring is an essential component of HIV treatment, commercially available tests rely on relatively high-resource chemistries like real-time polymerase chain reaction and are thus used on an infrequent basis for millions of people living with HIV in low-income countries. To address the constraints of low-resource settings on nucleic acid quantification, we describe a recombinase polymerase amplification and lateral flow detection approach that quantifies HIV-1 DNA or RNA by comparison to a competitive internal amplification control (IAC) of a known copy number, which may be set to any useful threshold (in our case, a clinically relevant threshold for HIV treatment failure). The IAC is designed to amplify alongside the HIV target with a similar efficiency, allowing for normalization of the assay to variation or inhibition and enabling an endpoint readout that is compatible with commercially available kits for nucleic acid lateral flow detection and interpretable with minimal instrumentation or by the naked eye. We find that this approach can reliably differentiate ≤600 or ≥1400 copies of HIV DNA from a 1000-copy threshold when lateral flow strips are imaged with a conventional office scanner and analyzed with free densitometry software. We further demonstrate a user-friendly adaptation of this analysis to process cell phone photographs with an automated script. Alternatively, we show via a survey that 21 minimally trained volunteers could reliably resolve ≥10-fold (log10) differences of HIV DNA or RNA by naked eye interpretation of lateral flow results. This amplification and detection workflow requires minimal instrumentation, takes just 30 min to complete, and when combined with a suitable sample preparation method, may enable HIV VL testing while the patient waits or a self-test, which has the potential to improve care. This approach may be adapted for other applications that require quantitative analysis of a nucleic acid target in low-resource settings.
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Affiliation(s)
- Ian T Hull
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Enos C Kline
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Gaurav K Gulati
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Jack Henry Kotnik
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Kamal G Shah
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Lisa Frenkel
- Department of Pediatrics, University of Washington, Seattle, Washington 98195-9300, United States.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195-7470, United States.,Department of Global Health, University of Washington, Seattle, Washington 98195-1620, United States.,Department of Medicine, University of Washington, Seattle, Washington 98195-6420, United States.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98145-5005, United States
| | - James Lai
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Joanne Stekler
- Department of Medicine, University of Washington, Seattle, Washington 98195-6420, United States
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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11
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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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12
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Wallner JJ, Beck IA, Panpradist N, Ruth PS, Valenzuela-Ponce H, Soto-Nava M, Ávila-Ríos S, Lutz BR, Frenkel LM. Rapid Near Point-of-Care Assay for HLA-B*57:01 Genotype Associated with Severe Hypersensitivity Reaction to Abacavir. AIDS Res Hum Retroviruses 2021; 37:930-935. [PMID: 34714103 DOI: 10.1089/aid.2021.0103] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The nucleoside reverse transcriptase inhibitor abacavir (ABC) is used commonly to treat young children with HIV infection and is a component of the fixed-dose-combination Triumeq®. ABC can trigger a severe hypersensitivity reaction in people who are homozygous or heterozygous for HLA-B*57:01. Testing for HLA-B*57:01 before ABC initiation is standard-of-care in high-resource settings, but current tests are costly or difficult to access in resource-limited settings. To address these gaps, we developed an inexpensive simple-to-use rapid assay to detect HLA-B*57:01. We designed and optimized a multiplexed polymerase chain reaction (PCR) to amplify HLA-B*57 subtypes and the human beta-globin gene; employed probes and ligation to specifically tag the HLA-B*57:01 allele with biotin. Tagged-ligated products were detected by immunocapture in an enzyme-linked immunosorbent assay plate or lateral flow strip. Cell lines with known HLA genotypes were used to optimize the assay. The optimized assay was then compared with genotypes of clinical specimens (n = 60) determined by sequencing, with specimens enriched for individuals with HLA-B*57:01. The optimized assay utilizes 40-min 35-cycle multiplex PCR for B*57 and beta-globin; 20-min ligation reaction; and 15-min detection. Evaluation of the HLA-B*57:01 oligonucleotide ligation assay using clinical specimens had a sensitivity of 100% (n = 27/27 typed as B*57:01) and specificity of 100% (n = 33/33 typed as non-B*57:01) by visual interpretation of lateral flow strips. The cost is US$5.96/specimen. This rapid and economical assay accurately detects HLA-B*57:01 in clinical specimens. Use of this assay could expand access to HLA-B*57:01 genotyping and facilitate safe same-day initiation of ABC-based treatment.
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Affiliation(s)
- Jackson J. Wallner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, USA
| | - Parker S. Ruth
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
| | - Humberto Valenzuela-Ponce
- CIENI Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Maribel Soto-Nava
- CIENI Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Santiago Ávila-Ríos
- CIENI Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Laboratory Medicine and Pathology, Global Health, and Medicine, Departments of Pediatrics, University of Washington, Seattle, Washington, USA
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13
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Oreskovic A, Waalkes A, Holmes EA, Rosenthal CA, Wilson DPK, Shapiro AE, Drain PK, Lutz BR, Salipante SJ. Characterizing the molecular composition and diagnostic potential of Mycobacterium tuberculosis urinary cell-free DNA using next-generation sequencing. Int J Infect Dis 2021; 112:330-337. [PMID: 34562627 PMCID: PMC8627387 DOI: 10.1016/j.ijid.2021.09.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Urine cell-free DNA (cfDNA) is an attractive target for diagnosing pulmonary Mycobacterium tuberculosis (MTB) infection, but has not been thoroughly characterized as a biomarker. METHODS This study was performed to investigate the size and composition of urine cfDNA from tuberculosis (TB) patients with minimal bias using next-generation sequencing (NGS). A combination of DNA extraction and single-stranded sequence library preparation methods demonstrated to recover short, highly degraded cfDNA fragments was employed. Urine cfDNA from 10 HIV-positive patients with pulmonary TB and two MTB-negative controls was examined. RESULTS MTB-derived cfDNA was identifiable by NGS from all MTB-positive patients and was absent from negative controls. MTB cfDNA was significantly shorter than human cfDNA, with median fragment lengths of ≤19-52 bp and 42-92 bp, respectively. MTB cfDNA abundance increased exponentially with decreased fragment length, having a peak fragment length of ≤19 bp in most samples. In addition, we identified a larger fraction of short human genomic cfDNA, ranging from 29 to 53 bp, than previously reported. Urine cfDNA fragments spanned the MTB genome with relative uniformity, but nucleic acids derived from multicopy elements were proportionately over-represented. CONCLUSIONS TB urine cfDNA is a potentially powerful biomarker but is highly fragmented, necessitating special procedures to maximize its recovery and detection.
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Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Elizabeth A Holmes
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Christopher A Rosenthal
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Douglas P K Wilson
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa; Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Adrienne E Shapiro
- Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Paul K Drain
- Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.
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14
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Gulati GK, Panpradist N, Stewart SWA, Beck IA, Boyce C, Oreskovic AK, García-Morales C, Avila-Ríos S, Han PD, Reyes-Terán G, Starita LM, Frenkel LM, Lutz BR, Lai JJ. Inexpensive workflow for simultaneous monitoring of HIV viral load and detection of SARS-CoV-2 infection. medRxiv 2021:2021.08.18.21256786. [PMID: 34462759 PMCID: PMC8404901 DOI: 10.1101/2021.08.18.21256786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
BACKGROUND COVID-19 pandemic interrupted routine care for individuals living with HIV, putting them at risk of becoming virologically unsuppressed and ill. Often they are at high risk for exposure to SARS-CoV-2 infection and severe disease once infected. For this population, it is urgent to closely monitor HIV plasma viral load ( VL ) and screen for SARS-COV-2 infection. METHOD We have developed a non-proprietary method to isolate RNA from plasma, nasal secretions ( NS ), or both. HIV, SARS-CoV-2, and human RP targets in extracted RNA are then RT-qPCR to estimate the VL and classify HIV/SARS-CoV-2 status ( i . e ., HIV as VL failure or suppressed; SARS-CoV-2 as positive, presumptive positive, negative, or indeterminate). We evaluated this workflow on 133 clinical specimens: 40 plasma specimens (30 HIV-seropositive), 67 NS specimens (31 SARS-CoV-2-positive), and 26 pooled plasma/NS specimens (26 HIV-positive with 10 SARS-CoV-2-positive), and compared the results obtained using the in-house extraction to those using a commercial extraction kit. RESULTS In-house extraction had a detection limit of 200-copies/mL for HIV and 100-copies/mL for SARS-CoV-2. In-house and commercial methods yielded positively correlated HIV VL (R 2 : 0.98 for contrived samples; 0.81 for seropositive plasma). SARS-CoV-2 detection had 100% concordant classifications in contrived samples, and in clinical NS extracted by in-house method, excluding indeterminate results, was 95% concordant (25 positives, 6 presumptive positives, and 31 negatives) to those using the commercial method. Analysis of pooled plasma/NS showed R 2 of 0.91 (contrived samples) and 0.71 (clinical specimens) for HIV VL correlations obtained by both extraction methods, while SARS-CoV-2 detection showed 100% concordance in contrived and clinical specimens. INTERPRETATION Our low-cost workflow for molecular testing of HIV and SARS-CoV-2 could serve as an alternative to current standard assays for laboratories in low-resource settings.
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15
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Kline EC, Panpradist N, Hull IT, Wang Q, Oreskovic AK, Han PD, Starita LM, Lutz BR. Multiplex Target-Redundant RT-LAMP for Robust Detection of SARS-CoV-2 Using Fluorescent Universal Displacement Probes. medRxiv 2021. [PMID: 34462755 DOI: 10.1101/2021.08.13.21261995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The increasing prevalence of variant lineages during the COVID-19 pandemic has the potential to disrupt molecular diagnostics due to mismatches between primers and variant templates. Point-of-care molecular diagnostics, which often lack the complete functionality of their high throughput laboratory counterparts, are particularly susceptible to this type of disruption, which can result in false negative results. To address this challenge, we have developed a robust Loop Mediated Isothermal Amplification assay with single tube multiplexed multi-target redundancy and an internal amplification control. A convenient and cost-effective target specific fluorescence detection system allows amplifications to be grouped by signal using adaptable probes for pooled reporting of SARS-COV-2 target amplifications or differentiation of the Internal Amplification Control. Over the course of the pandemic, primer coverage of viral lineages by the three redundant sub-assays has varied from assay to assay as they have diverged from the Wuhan-Hu-1 isolate sequence, but aggregate coverage has remained high for all variant sequences analyzed, with a minimum of 97.4% (Variant of Interest: Eta). In three instances (Delta, Gamma, Eta), a high frequency mismatch with one of the three sub-assays was observed, but overall coverage remained high due to multi-target redundancy. When challenged with extracted human samples the multiplexed assay showed 100% sensitivity for samples containing greater than 30 copies of viral RNA per reaction, and 100% specificity. These results are further evidence that conventional laboratory methodologies can be leveraged at the point-of-care for robust performance and diagnostic stability over time.
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16
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Oreskovic A, Panpradist N, Marangu D, Ngwane MW, Magcaba ZP, Ngcobo S, Ngcobo Z, Horne DJ, Wilson DPK, Shapiro AE, Drain PK, Lutz BR. Diagnosing Pulmonary Tuberculosis by Using Sequence-Specific Purification of Urine Cell-Free DNA. J Clin Microbiol 2021; 59:e0007421. [PMID: 33789959 PMCID: PMC8373247 DOI: 10.1128/jcm.00074-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 01/25/2021] [Accepted: 03/19/2021] [Indexed: 01/17/2023] Open
Abstract
Transrenal urine cell-free DNA (cfDNA) is a promising tuberculosis (TB) biomarker, but is challenging to detect because of the short length (<100 bp) and low concentration of TB-specific fragments. We aimed to improve the diagnostic sensitivity of TB urine cfDNA by increasing recovery of short fragments during sample preparation. We developed a highly sensitive sequence-specific purification method that uses hybridization probes immobilized on magnetic beads to capture short TB cfDNA (50 bp) with 91.8% average efficiency. Combined with short-target PCR, the assay limit of detection was ≤5 copies of cfDNA in 10 ml urine. In a clinical cohort study in South Africa, our urine cfDNA assay had 83.7% sensitivity (95% CI: 71.0 to 91.5%) and 100% specificity (95% CI: 86.2 to 100%) for diagnosis of active pulmonary TB when using sputum Xpert MTB/RIF as the reference standard. The detected cfDNA concentration was 0.14 to 2,804 copies/ml (median 14.6 copies/ml) and was inversely correlated with CD4 count and days to culture positivity. Sensitivity was nonsignificantly higher in HIV-positive (88.2%) compared to HIV-negative patients (73.3%), and was not dependent on CD4 count. Sensitivity remained high in sputum smear-negative (76.0%) and urine lipoarabinomannan (LAM)-negative (76.5%) patients. With improved sample preparation, urine cfDNA is a viable biomarker for TB diagnosis. Our assay has the highest reported accuracy of any TB urine cfDNA test to date and has the potential to enable rapid non-sputum-based TB diagnosis across key underserved patient populations.
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Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Diana Marangu
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - M. William Ngwane
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
| | - Zanele P. Magcaba
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
| | - Sindiswa Ngcobo
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
| | - Zinhle Ngcobo
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
| | - David J. Horne
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Douglas P. K. Wilson
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
- Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Adrienne E. Shapiro
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Paul K. Drain
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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17
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Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, Kozodoy L, Carter L, Ravichandran R, Green LB, Matochko WL, Thomson CA, Vögeli B, Krüger-Gericke A, VanBlargan LA, Chen RE, Ying B, Bailey AL, Kafai NM, Boyken S, Ljubetič A, Edman N, Ueda G, Chow C, Addetia A, Panpradist N, Gale M, Freedman BS, Lutz BR, Bloom JD, Ruohola-Baker H, Whelan SPJ, Stewart L, Diamond MS, Veesler D, Jewett MC, Baker D. Multivalent designed proteins protect against SARS-CoV-2 variants of concern. bioRxiv 2021:2021.07.07.451375. [PMID: 34268509 PMCID: PMC8282097 DOI: 10.1101/2021.07.07.451375] [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: 12/27/2022]
Abstract
Escape variants of SARS-CoV-2 are threatening to prolong the COVID-19 pandemic. To address this challenge, we developed multivalent protein-based minibinders as potential prophylactic and therapeutic agents. Homotrimers of single minibinders and fusions of three distinct minibinders were designed to geometrically match the SARS-CoV-2 spike (S) trimer architecture and were optimized by cell-free expression and found to exhibit virtually no measurable dissociation upon binding. Cryo-electron microscopy (cryoEM) showed that these trivalent minibinders engage all three receptor binding domains on a single S trimer. The top candidates neutralize SARS-CoV-2 variants of concern with IC 50 values in the low pM range, resist viral escape, and provide protection in highly vulnerable human ACE2-expressing transgenic mice, both prophylactically and therapeutically. Our integrated workflow promises to accelerate the design of mutationally resilient therapeutics for pandemic preparedness. ONE-SENTENCE SUMMARY We designed, developed, and characterized potent, trivalent miniprotein binders that provide prophylactic and therapeutic protection against emerging SARS-CoV-2 variants of concern.
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Affiliation(s)
- Andrew C. Hunt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Shally Saini
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Louisa Helms
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology and Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, 98195, USA
| | - Tien-Ying Hsiang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Tyler N. Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lisa Kozodoy
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | | | | | | | - Bastain Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Antje Krüger-Gericke
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Baoling Ying
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Adam L. Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Natasha M. Kafai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott Boyken
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ajasja Ljubetič
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Natasha Edman
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cameron Chow
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- The Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin S. Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
- Division of Nephrology and Kidney Research Institute, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
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18
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Beidler PG, Novokhodko A, Prolo LM, Browd S, Lutz BR. Fluidic Considerations of Measuring Intracranial Pressure Using an Open External Ventricular Drain. Cureus 2021; 13:e15324. [PMID: 34221772 PMCID: PMC8239198 DOI: 10.7759/cureus.15324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Measurement of intracranial pressure (ICP) during cerebrospinal fluid (CSF) drainage with an external ventricular drain (EVD) typically requires stopping the flow during measurement. However, there may be benefits to simultaneous ICP measurement and CSF drainage. Several studies have evaluated whether accurate ICP measurements can be obtained while the EVD is open. They report differing outcomes when it comes to error, and hypothesize several sources of error. This study presents an investigation into the fluidic sources of error for ICP measurement with concurrent drainage in an EVD. Our experiments and analytical model both show that the error in pressure measurement increases linearly with flow rate and is not clinically significant, regardless of drip chamber height. At physiologically relevant flow rates (40 mL/hr) and ICP set points (13.6 - 31.3 cmH2O or 10 - 23 mmHg), our model predicts an underestimation of 0.767 cmH2O (0.56 mmHg) with no observed data point showing error greater than 1.09 cmH2O (0.8 mmHg) in our experiment. We extrapolate our model to predict a realistic worst-case clinical scenario where we expect to see a mean maximum error of 1.06 cmH2O (0.78 mmHg) arising from fluidic effects within the drainage system for the most resistive catheter. Compared to other sources of error in current ICP monitoring, error in pressure measurement due to drainage flow is small and does not prohibit clinical use. However, other effects such as ventricular collapse or catheter obstruction could affect ICP measurement under continuous drainage and are not investigated in this study.
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Affiliation(s)
| | - Alexander Novokhodko
- Bioengineering, University of Washington, Seattle, USA.,Mechanical Engineering, University of Washington, Seattle, USA
| | - Laura M Prolo
- Neurosurgery, Stanford University School of Medicine, Stanford, USA.,Surgical Services, VA Palo Alto Health Care System, Palo Alto, USA
| | - Samuel Browd
- Neurosurgery, Seattle Children's Hospital, Seattle, USA.,Bioengineering, University of Washington, Seattle, USA.,Neurological Surgery, University of Washington, Seattle, USA
| | - Barry R Lutz
- Bioengineering, University of Washington, Seattle, USA
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19
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Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Ilcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Sci Transl Med 2021; 13:eabf0202. [PMID: 33941621 PMCID: PMC8158963 DOI: 10.1126/scitranslmed.abf0202] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 09/29/2020] [Revised: 01/23/2021] [Accepted: 04/25/2021] [Indexed: 12/16/2022]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gravely affected societies around the world. Outbreaks in different parts of the globe have been shaped by repeated introductions of new viral lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State (USA) to characterize how the spread of SARS-CoV-2 in Washington State in early 2020 was shaped by differences in timing of mitigation strategies across counties and by repeated introductions of viral lineages into the state. In addition, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G but not the other variant (614D) into the state. At an individual level, we observed evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we did not find any evidence that the 614G variant affects clinical severity or patient outcomes. Overall, this suggests that with regard to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus.
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Affiliation(s)
- Nicola F Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Cassia Wagner
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Chris D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Louise H Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Benjamin Pelle
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew Richardson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Erica Ryke
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Victoria M Rachleff
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Elisabeth Brandstetter
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Peter D Han
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kirsten Lacombe
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Caitlin R Wolf
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | | | - Barry R Lutz
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Matthew Thompson
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey S Duchin
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Public Health - Seattle & King County, Seattle, WA98121, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Helen Y Chu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Scott Lindquist
- Washington State Department of Health, Shoreline, WA 98155, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
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20
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Oreskovic A, Lutz BR. Ultrasensitive hybridization capture: Reliable detection of <1 copy/mL short cell-free DNA from large-volume urine samples. PLoS One 2021; 16:e0247851. [PMID: 33635932 PMCID: PMC7909704 DOI: 10.1371/journal.pone.0247851] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/12/2021] [Indexed: 12/19/2022] Open
Abstract
Urine cell-free DNA (cfDNA) is a valuable non-invasive biomarker with broad potential clinical applications, but there is no consensus on its optimal pre-analytical methodology, including the DNA extraction step. Due to its short length (majority of fragments <100 bp) and low concentration (ng/mL), urine cfDNA is not efficiently recovered by conventional silica-based extraction methods. To maximize sensitivity of urine cfDNA assays, we developed an ultrasensitive hybridization method that uses sequence-specific oligonucleotide capture probes immobilized on magnetic beads to improve extraction of short cfDNA from large-volume urine samples. Our hybridization method recovers near 100% (95% CI: 82.6-117.6%) of target-specific DNA from 10 mL urine, independent of fragment length (25-150 bp), and has a limit of detection of ≤5 copies of double-stranded DNA (0.5 copies/mL). Pairing hybridization with an ultrashort qPCR design, we can efficiently capture and amplify fragments as short as 25 bp. Our method enables amplification of cfDNA from 10 mL urine in a single qPCR well, tolerates variation in sample composition, and effectively removes non-target DNA. Our hybridization protocol improves upon both existing silica-based urine cfDNA extraction methods and previous hybridization-based sample preparation protocols. Two key innovations contribute to the strong performance of our method: a two-probe system enabling recovery of both strands of double-stranded DNA and dual biotinylated capture probes, which ensure consistent, high recovery by facilitating optimal probe density on the bead surface, improving thermostability of the probe-bead linkage, and eliminating interference by endogenous biotin. We originally designed the hybridization method for tuberculosis diagnosis from urine cfDNA, but expect that it will be versatile across urine cfDNA targets, and may be useful for other cfDNA sample types and applications beyond cfDNA. To make our hybridization method accessible to new users, we present a detailed protocol and straightforward guidelines for designing new capture probes.
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Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
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21
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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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22
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Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Llcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. medRxiv 2020:2020.09.30.20204230. [PMID: 33024981 PMCID: PMC7536883 DOI: 10.1101/2020.09.30.20204230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 01/12/2023]
Abstract
The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.
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Affiliation(s)
| | - Cassia Wagner
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | - Pavitra Roychoudhury
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Jover Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | - Erica Ryke
- University of Washington, Seattle, WA, USA
| | - Hong Xie
- University of Washington, Seattle, WA, USA
| | | | | | - Victoria M Rachleff
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | | | - Romesh Gautom
- Washington State Department of Health, Shoreline, WA, USA
| | - Geoff Melly
- Washington State Department of Health, Shoreline, WA, USA
| | - Brian Hiatt
- Washington State Department of Health, Shoreline, WA, USA
| | - Philip Dykema
- Washington State Department of Health, Shoreline, WA, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Kairsten Fay
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Misja Llcisin
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | | | | | - Michael Boeckh
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Janet A Englund
- University of Washington, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Barry R Lutz
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Jeffrey S Duchin
- University of Washington, Seattle, WA, USA
- Public Health - Seattle & King County, Seattle, WA, USA
| | - Lea M Starita
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Helen Y Chu
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Jay Shendure
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Keith R Jerome
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | - Alexander L Greninger
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Deborah A Nickerson
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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23
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Panpradist N, Beck IA, Vrana J, Higa N, McIntyre D, Ruth PS, So I, Kline EC, Kanthula R, Wong-On-Wing A, Lim J, Ko D, Milne R, Rossouw T, Feucht UD, Chung M, Jourdain G, Ngo-Giang-Huong N, Laomanit L, Soria J, Lai J, Klavins ED, Frenkel LM, Lutz BR. OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories. EBioMedicine 2019; 50:34-44. [PMID: 31767540 PMCID: PMC6921160 DOI: 10.1016/j.ebiom.2019.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/21/2023] Open
Abstract
Background HIV drug resistance (HIVDR) testing can assist clinicians in selecting treatments. However, high complexity and cost of genotyping assays limit routine testing in settings where HIVDR prevalence has reached high levels. Methods The oligonucleotide ligation assay (OLA)-Simple kit was developed for detection of HIVDR against first-line non-nucleoside/nucleoside reverse transcriptase inhibitors and validated on 672 codons (168 specimens) from subtypes A, B, C, D, and AE. The kit uses dry reagents to facilitate assay setup, lateral flow devices for visual HIVDR detections, and in-house software with an interface for guiding users and analyzing results. Findings HIVDR analysis of specimens by OLA-Simple compared to Sanger sequencing revealed 99.6 ± 0.3% specificity and 98.2 ± 0.9% sensitivity, and compared to high-sensitivity assays, 99.6 ± 0.6% specificity and 86.2 ± 2.5% sensitivity, with 2.6 ± 0.9% indeterminate results. OLA-Simple was performed more rapidly compared to Sanger sequencing (<4 h vs. 35–72 h). Forty-one untrained volunteers blindly tested two specimens each with 96.8 ± 0.8% accuracy. Interpretation OLA-Simple compares favorably with HIVDR genotyping by Sanger and sensitive comparators. Instructional software enabled inexperienced, first-time users to perform the assay with high accuracy. The reduced complexity, cost, and training requirements of OLA-Simple could improve access to HIVDR testing in low-resource settings and potentially allow same-day selection of appropriate antiretroviral therapy. Fund USA National Institutes of Health R01; the Clinical and Retrovirology Research Core and the Molecular Profiling and Computational Biology Core of the UW CFAR; Seattle Children's Research Institute; UW Holloman Innovation Challenge Award; Pilcher Faculty Fellowship.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Global WACh Program, Department of Global Health, University of Washington, Seattle, WA 98104, USA
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Justin Vrana
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Nikki Higa
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - David McIntyre
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Parker S Ruth
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Isaac So
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Enos C Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ruth Kanthula
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Medstar Georgetown University Hospital, DC, 20007, USA
| | - Annie Wong-On-Wing
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Jonathan Lim
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Daisy Ko
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ross Milne
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Theresa Rossouw
- Department of Immunology, University of Pretoria, Pretoria 0002, South Africa
| | - Ute D Feucht
- Research Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, Department of Paediatrics, University of Pretoria, Pretoria 0002, South Africa; Research Unit for Maternal and Infant Health Care Strategies, South African Medical Research Council, Kalafong Hospital, Atteridgeville 0008, South Africa
| | - Michael Chung
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Epidemiology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Medicine, Aga Khan University, Nairobi, Kenya
| | - Gonzague Jourdain
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Laddawan Laomanit
- Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Jaime Soria
- Department of Infectious Diseases, Hospital Nacional Dos de Mayo, Av. Miguel Grau 13, Cercado de Lima 15003, Peru
| | - James Lai
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Eric D Klavins
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Division of Infectious Diseases, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Virology, Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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Chu HY, Chu HY, Boeckh M, Boeckh M, Englund JA, Englund JA, Famulare M, Lutz BR, Lutz BR, Nickerson DA, Rieder M, Rieder M, Starita L, Starita L, Thompson M, Thompson M, Shendure J, Bedford T, Adler A, Brandstetter E, Brandstetter E, Bosua J, Bosua J, Frazar CD, Han PD, Gulati R, Hadfield J, Huang S, Jackson ML, Jackson ML, Kiavand A, Kimball LE, Kimball LE, Lacombe K, Lacombe K, Logue J, Logue J, Lyon V, Sibley TR, Zigman Suchsland ML, Zigman Suchsland ML, Wolf CR, Wolf CR. LB21. The Seattle Flu Study: A Community-Based Study of Influenza. Open Forum Infect Dis 2019. [PMCID: PMC6809800 DOI: 10.1093/ofid/ofz415.2504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect and contain new and emerging flu strains at a population level. The objective of this study was to use data gathered simultaneously from community and hospital sites to develop a model of how flu enters and spreads in a population.
Methods
In the 2018–2019 season, we enrolled individuals with respiratory illness from community sites throughout the Seattle area, including homeless shelters, childcare facilities, Seattle-Tacoma International Airport, workplaces, college campuses, clinics, and at home (Figure 1). We collected data and nasal swabs from individuals with at least two respiratory symptoms. Additionally, we collected residual nasal swabs and data from individuals who sought care at four regional hospitals. Home-based self-testing for influenza and prediction models for influenza were piloted. Swabs were tested with a multiplex molecular assay, and influenza whole-genome sequencing was performed. Geospatial mapping and computational modeling platforms were developed to characterize regional spread of respiratory pathogens.
Results
A total of 18,847 samples were collected in the 2018–2019 season. Of those tested to date, 291/3,653 (8%) community and 2,393/11,273 (21%) hospital samples have influenza detected. Of the community enrollments, 39% had influenza-like illness. Community enrollees were in age groups not well-represented from hospitals. Influenza A/H3N2 activity peaked on college campuses and homeless shelters 2 weeks before the peak in hospitals. We observed multiple independent introductions of influenza strains into the city and evidence of sustained transmission chains within the city (Figures 2 and 3).
Conclusion
Utilizing the city-wide infrastructure we developed, we observed the introduction of influenza A/H3N2 into the community before the hospital and evidence of transmissions of unique strains into and within the Seattle area. These data provide the blueprint for implementing city-wide, community-based surveillance systems for rapid detection, real-time assessment of transmission patterns, and interruption of spread of seasonal or pandemic strains.
Disclosures
Helen Y. Chu, MD MPH, Merck (Advisor or Review Panel member), Michael Boeckh, MD PhD, Ablynx (Consultant, Grant/Research Support), Ansun Biopharma (Consultant, Grant/Research Support), Bavarian Nordic (Consultant), Gilead (Consultant, Grant/Research Support), GlaxoSmithKline (Consultant), Vir Bio (Consultant, Grant/Research Support), Janet A. Englund, MD, Chimerix (Grant/Research Support), GlaxoSmithKline (Grant/Research Support), MedImmune/Astrazeneca (Grant/Research Support), Meissa Vaccines (Consultant), Merck (Grant/Research Support),Novavax (Grant/Research Support), Sanofi Pastuer (Consultant), Matthew Thompson, MD, Alere Inc. (Research Grant or Support), Roche Molecular Diagnostics (Consultant, Research Grant or Support, Speaker’s Bureau), . Other Authors: No reported disclosures.
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Affiliation(s)
- Helen Y Chu
- University of Washington, Seattle, Washington
| | - Helen Y Chu
- University of Washington, Seattle, Washington
| | - Michael Boeckh
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Michael Boeckh
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Janet A Englund
- Seattle Children’s Hospital/University of Washington, Seattle, Washington
| | - Janet A Englund
- Seattle Children’s Hospital/University of Washington, Seattle, Washington
| | | | | | | | | | - Mark Rieder
- University of Washington, Seattle, Washington
| | - Mark Rieder
- University of Washington, Seattle, Washington
| | - Lea Starita
- University of Washington, Seattle, Washington
| | - Lea Starita
- University of Washington, Seattle, Washington
| | | | | | | | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Amanda Adler
- Seattle Children’s Research Institute, Seattle, Washington
| | | | | | - Jeris Bosua
- University of Washington, Seattle, Washington
| | - Jeris Bosua
- University of Washington, Seattle, Washington
| | | | - Peter D Han
- University of Washington, Seattle, Washington
| | - Reena Gulati
- DGMQ/Centers for Disease Control and Prevention, Seattle, Washington
| | - James Hadfield
- Fred Hutchinson Cancer Research Center, Seattle, Washington
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Thompson M, Zigman Suchsland ML, Lyon V, Kline E, Huang S, Chu HY, Rieder M, Starita L, Bosua J, Lutz BR. 1775. A Community-wide Study to Evaluate the Accuracy of Self-testing for Influenza: Works in Progress. Open Forum Infect Dis 2019. [PMCID: PMC6808943 DOI: 10.1093/ofid/ofz360.1638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Seasonal influenza (flu) occurs annually, causing disease with substantial morbidity and mortality. Currently, flu is suspected from clinical features, but requires a laboratory test to confirm infection. No influenza tests in the United States are approved for use outside of clinical settings. We aimed to determine the accuracy of influenza self-testing using an at-home, app-guided, lateral flow assay compared with a molecular reference standard conducted at a laboratory among adults self-reporting influenza-like illness (ILI).
Methods
This is an observational study of individuals with self-reported ILI throughout the continental 48 United States recruited from the Flu Near You platform, online marketing, and clinics in the Seattle area. Recruitment took place from March 4 to April 26, 2019. Participants were directed to an iPhone App that determined eligibility, consent, and responses to symptom questions and risk factors. Individuals were mailed a commercially available CLIA-waived influenza lateral flow test to conduct at home, guided by the app, and returned the used test along with a second nasal swab collected in viral transport media to the research team. Influenza testing was performed by RT–PCR on the second nasal swab, as well as the residual fluid from the RDT. Accuracy of home test result (read by the participant), as well as image capture of the lateral flow test strip, were compared with the lab-based reference standard.
Results
To date, 1127 at-home flu tests were mailed to participants and 711 (63.1%) samples returned to the lab. There were 17 flu-positive results from the rapid diagnostic test for a flu positivity rate of 2.4%. Testing using the reference standard is currently in progress. We will share diagnostic accuracy results once testing of the reference standard is completed. Of the kits returned, 353 (49.7%)had an error recorded, which included errors in return packaging, reference standard, rapid test tube sample, or rapid test strip errors.
Conclusion
Overall, findings from this study will determine the accuracy of an at-home rapid diagnostic test, and inform more widely research design for evaluating smartphone-enhanced home tests for pathogens. Many samples returned to the lab had a recorded error, suggesting at-home testing requires additional feasibility testing and refinement of the current methods used.
Disclosures
All authors: No reported disclosures.
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Affiliation(s)
| | | | | | - Enos Kline
- University of Washington, Seattle, Washington
| | | | - Helen Y Chu
- University of Washington, Seattle, Washington
| | | | - Lea Starita
- University of Washington, Seattle, Washington
| | - Jeris Bosua
- University of Washington, Seattle, Washington
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Oreskovic A, Brault ND, Panpradist N, Lai JJ, Lutz BR. Analytical Comparison of Methods for Extraction of Short Cell-Free DNA from Urine. J Mol Diagn 2019; 21:1067-1078. [PMID: 31442674 DOI: 10.1016/j.jmoldx.2019.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 11/19/2022] Open
Abstract
Urine cell-free DNA (cfDNA) is a valuable noninvasive biomarker for cancer mutation detection, infectious disease diagnosis (eg, tuberculosis), organ transplantation monitoring, and prenatal screening. Conventional silica DNA extraction does not efficiently capture urine cfDNA, which is dilute (ng/mL) and highly fragmented [30 to 100 nucleotides (nt)]. The clinical sensitivity of urine cfDNA detection increases with decreasing target length, motivating use of sample preparation methods designed for short fragments. We compared the analytical performance of two published protocols (Wizard resin/guanidinium thiocyanate and Q Sepharose), three commercial kits (Norgen, QIAamp, and MagMAX), and an in-house sequence-specific hybridization capture technique. Dependence on fragment length (25 to 150 nt), performance at low concentrations (10 copies/mL), tolerance to variable urine conditions, and susceptibility to PCR inhibition were characterized. Hybridization capture and Q Sepharose performed best overall (60% to 90% recovery), although Q Sepharose had reduced recovery (<10%) of the shortest 25-nt fragment. Wizard resin/guanidinium thiocyanate recovery was dependent on pH and background DNA concentration and was limited to <35%, even under optimal conditions. The Norgen kit led to consistent PCR inhibition but had high recovery of short fragments. The QIAamp and MagMAX kits had minimal recovery of fragments <150 and <80 nt, respectively. Urine cfDNA extraction methods differ widely in ability to capture short, dilute cfDNA in urine; using suboptimal methods may profoundly impair clinical results.
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Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Norman D Brault
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - James J Lai
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington.
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27
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Lafleur LK, Bishop JD, Heiniger EK, Gallagher RP, Wheeler MD, Kauffman P, Zhang X, Kline EC, Buser JR, Kumar S, Byrnes SA, Vermeulen NMJ, Scarr NK, Belousov Y, Mahoney W, Toley BJ, Ladd PD, Lutz BR, Yager P. A rapid, instrument-free, sample-to-result nucleic acid amplification test. Lab Chip 2016; 16:3777-87. [PMID: 27549897 DOI: 10.1039/c6lc00677a] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The prototype demonstrated here is the first fully integrated sample-to-result diagnostic platform for performing nucleic acid amplification tests that requires no permanent instrument or manual sample processing. The multiplexable autonomous disposable nucleic acid amplification test (MAD NAAT) is based on two-dimensional paper networks, which enable sensitive chemical detection normally reserved for laboratories to be carried out anywhere by untrained users. All reagents are stored dry in the disposable test device and are rehydrated by stored buffer. The paper network is physically multiplexed to allow independent isothermal amplification of multiple targets; each amplification reaction is also chemically multiplexed with an internal amplification control. The total test time is less than one hour. The MAD NAAT prototype was used to characterize a set of human nasal swab specimens pre-screened for methicillin-resistant Staphylococcus aureus (MRSA) bacteria. With qPCR as the quantitative reference method, the lowest input copy number in the range where the MAD NAAT prototype consistently detected MRSA in these specimens was ∼5 × 10(3) genomic copies (∼600 genomic copies per biplexed amplification reaction).
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Affiliation(s)
- Lisa K Lafleur
- Department of Bioengineering, University of Washington, Seattle, USA.
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Venkataraman P, Browd SR, Lutz BR. A physical framework for implementing virtual models of intracranial pressure and cerebrospinal fluid dynamics in hydrocephalus shunt testing. J Neurosurg Pediatr 2016; 18:296-305. [PMID: 27203135 DOI: 10.3171/2016.2.peds15478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE The surgical placement of a shunt designed to resolve the brain's impaired ability to drain excess CSF is one of the most common treatments for hydrocephalus. The use of a dynamic testing platform is an important part of shunt testing that can faithfully reproduce the physiological environment of the implanted shunts. METHODS A simulation-based framework that serves as a proof of concept for enabling the application of virtual intracranial pressure (ICP) and CSF models to a physical shunt-testing system was engineered. This was achieved by designing hardware and software that enabled the application of dynamic model-driven inlet and outlet pressures to a shunt and the subsequent measurement of the resulting drainage rate. RESULTS A set of common physiological scenarios was simulated, including oscillations in ICP due to respiratory and cardiac cycles, changes in baseline ICP due to changes in patient posture, and transient ICP spikes caused by activities such as exercise, coughing, sneezing, and the Valsalva maneuver. The behavior of the Strata valve under a few of these physiological conditions is also demonstrated. CONCLUSIONS Testing shunts with dynamic ICP and CSF simulations can facilitate the optimization of shunts to be more failure resistant and better suited to patient physiology.
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Affiliation(s)
| | - Samuel R Browd
- Division of Pediatric Neurosurgery, Seattle Children's Hospital, Seattle, Washington
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle; and
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29
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Phillips RH, Jain R, Browning Y, Shah R, Kauffman P, Dinh D, Lutz BR. Flow control using audio tones in resonant microfluidic networks: towards cell-phone controlled lab-on-a-chip devices. Lab Chip 2016; 16:3260-7. [PMID: 27416111 DOI: 10.1039/c6lc00738d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Fluid control remains a challenge in development of portable lab-on-a-chip devices. Here, we show that microfluidic networks driven by single-frequency audio tones create resonant oscillating flow that is predicted by equivalent electrical circuit models. We fabricated microfluidic devices with fluidic resistors (R), inductors (L), and capacitors (C) to create RLC networks with band-pass resonance in the audible frequency range available on portable audio devices. Microfluidic devices were fabricated from laser-cut adhesive plastic, and a "buzzer" was glued to a diaphragm (capacitor) to integrate the actuator on the device. The AC flowrate magnitude was measured by imaging oscillation of bead tracers to allow direct comparison to the RLC circuit model across the frequency range. We present a systematic build-up from single-channel systems to multi-channel (3-channel) networks, and show that RLC circuit models predict complex frequency-dependent interactions within multi-channel networks. Finally, we show that adding flow rectifying valves to the network creates pumps that can be driven by amplified and non-amplified audio tones from common audio devices (iPod and iPhone). This work shows that RLC circuit models predict resonant flow responses in multi-channel fluidic networks as a step towards microfluidic devices controlled by audio tones.
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Affiliation(s)
- Reid H Phillips
- Department of Bioengineering, University of Washington, Box 355061, Foege N530N, 3720 15th Ave NE, Seattle, WA 98195, USA.
| | - Rahil Jain
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Yoni Browning
- Department of Bioengineering, University of Washington, Box 355061, Foege N530N, 3720 15th Ave NE, Seattle, WA 98195, USA.
| | - Rachana Shah
- Department of Bioengineering, University of Washington, Box 355061, Foege N530N, 3720 15th Ave NE, Seattle, WA 98195, USA.
| | - Peter Kauffman
- Department of Bioengineering, University of Washington, Box 355061, Foege N530N, 3720 15th Ave NE, Seattle, WA 98195, USA.
| | - Doan Dinh
- Department of Bioengineering, University of Washington, Box 355061, Foege N530N, 3720 15th Ave NE, Seattle, WA 98195, USA.
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Box 355061, Foege N530N, 3720 15th Ave NE, Seattle, WA 98195, USA.
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Panpradist N, Beck IA, Chung MH, Kiarie JN, Frenkel LM, Lutz BR. Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation. PLoS One 2016; 11:e0145962. [PMID: 26751207 PMCID: PMC4713472 DOI: 10.1371/journal.pone.0145962] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 05/20/2015] [Accepted: 12/10/2015] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA) is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1) lysis and/or nucleic acid extraction, (2) amplification of HIV RNA or DNA, (3) ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4) analysis via oligonucleotide surface capture, denaturation, and detection (CDD). The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A) in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Ingrid A. Beck
- Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Michael H. Chung
- Department of Internal Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - James N. Kiarie
- Departments of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - Lisa M. Frenkel
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Departments of Pediatrics and Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Toley BJ, Wang JA, Gupta M, Buser JR, Lafleur LK, Lutz BR, Fu E, Yager P. A versatile valving toolkit for automating fluidic operations in paper microfluidic devices. Lab Chip 2015; 15:1432-44. [PMID: 25606810 PMCID: PMC4391506 DOI: 10.1039/c4lc01155d] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Failure to utilize valving and automation techniques has restricted the complexity of fluidic operations that can be performed in paper microfluidic devices. We developed a toolkit of paper microfluidic valves and methods for automatic valve actuation using movable paper strips and fluid-triggered expanding elements. To the best of our knowledge, this is the first functional demonstration of this valving strategy in paper microfluidics. After introduction of fluids on devices, valves can actuate automatically after a) a certain period of time, or b) the passage of a certain volume of fluid. Timing of valve actuation can be tuned with greater than 8.5% accuracy by changing lengths of timing wicks, and we present timed on-valves, off-valves, and diversion (channel-switching) valves. The actuators require ~30 μl fluid to actuate and the time required to switch from one state to another ranges from ~5 s for short to ~50 s for longer wicks. For volume-metered actuation, the size of a metering pad can be adjusted to tune actuation volume, and we present two methods - both methods can achieve greater than 9% accuracy. Finally, we demonstrate the use of these valves in a device that conducts a multi-step assay for the detection of the malaria protein PfHRP2. Although slightly more complex than devices that do not have moving parts, this valving and automation toolkit considerably expands the capabilities of paper microfluidic devices. Components of this toolkit can be used to conduct arbitrarily complex, multi-step fluidic operations on paper-based devices, as demonstrated in the malaria assay device.
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Affiliation(s)
- Bhushan J Toley
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA.
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32
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Toley BJ, Covelli I, Belousov Y, Ramachandran S, Kline E, Scarr N, Vermeulen N, Mahoney W, Lutz BR, Yager P. Isothermal strand displacement amplification (iSDA): a rapid and sensitive method of nucleic acid amplification for point-of-care diagnosis. Analyst 2015; 140:7540-9. [DOI: 10.1039/c5an01632k] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A new rapid and sensitive method of isothermal DNA amplification and a simple kinetic model of this reaction network.
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Affiliation(s)
| | - Isabela Covelli
- Department of Bioengineering
- University of Washington
- Seattle
- USA
| | | | | | - Enos Kline
- Department of Bioengineering
- University of Washington
- Seattle
- USA
| | - Noah Scarr
- ELITechGroup Inc. Molecular Diagnostics
- Bothell
- USA
| | | | - Walt Mahoney
- ELITechGroup Inc. Molecular Diagnostics
- Bothell
- USA
| | - Barry R. Lutz
- Department of Bioengineering
- University of Washington
- Seattle
- USA
| | - Paul Yager
- Department of Bioengineering
- University of Washington
- Seattle
- USA
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Panpradist N, Toley BJ, Zhang X, Byrnes S, Buser JR, Englund JA, Lutz BR. Swab sample transfer for point-of-care diagnostics: characterization of swab types and manual agitation methods. PLoS One 2014; 9:e105786. [PMID: 25181250 PMCID: PMC4152222 DOI: 10.1371/journal.pone.0105786] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 07/24/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The global need for disease detection and control has increased effort to engineer point-of-care (POC) tests that are simple, robust, affordable, and non-instrumented. In many POC tests, sample collection involves swabbing the site (e.g., nose, skin), agitating the swab in a fluid to release the sample, and transferring the fluid to a device for analysis. Poor performance in sample transfer can reduce sensitivity and reproducibility. METHODS In this study, we compared bacterial release efficiency of seven swab types using manual-agitation methods typical of POC devices. Transfer efficiency was measured using quantitative PCR (qPCR) for Staphylococcus aureus under conditions representing a range of sampling scenarios: 1) spiking low-volume samples onto the swab, 2) submerging the swab in excess-volume samples, and 3) swabbing dried sample from a surface. RESULTS Excess-volume samples gave the expected recovery for most swabs (based on tip fluid capacity); a polyurethane swab showed enhanced recovery, suggesting an ability to accumulate organisms during sampling. Dry samples led to recovery of ∼20-30% for all swabs tested, suggesting that swab structure and volume is less important when organisms are applied to the outer swab surface. Low-volume samples led to the widest range of transfer efficiencies between swab types. Rayon swabs (63 µL capacity) performed well for excess-volume samples, but showed poor recovery for low-volume samples. Nylon (100 µL) and polyester swabs (27 µL) showed intermediate recovery for low-volume and excess-volume samples. Polyurethane swabs (16 µL) showed excellent recovery for all sample types. This work demonstrates that swab transfer efficiency can be affected by swab material, structure, and fluid capacity and details of the sample. Results and quantitative analysis methods from this study will assist POC assay developers in selecting appropriate swab types and transfer methods.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Bhushan J. Toley
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Xiaohong Zhang
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Samantha Byrnes
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Joshua R. Buser
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Janet A. Englund
- Program in Infectious Diseases, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington, Seattle, Washington, United States of America
- * E-mail: (JAE); (BRL)
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- * E-mail: (JAE); (BRL)
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Lutz BR, Venkataraman P, Browd SR. New and improved ways to treat hydrocephalus: Pursuit of a smart shunt. Surg Neurol Int 2013; 4:S38-50. [PMID: 23653889 PMCID: PMC3642745 DOI: 10.4103/2152-7806.109197] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 11/08/2012] [Indexed: 11/14/2022] Open
Abstract
The most common treatment for hydrocephalus is placement of a cerebrospinal fluid shunt to supplement or replace lost drainage capacity. Shunts are life-saving devices but are notorious for high failure rates, difficulty of diagnosing failure, and limited control options. Shunt designs have changed little since their introduction in 1950s, and the few changes introduced have had little to no impact on these long-standing problems. For decades, the community has envisioned a “smart shunt” that could provide advanced control, diagnostics, and communication based on implanted sensors, feedback control, and telemetry. The most emphasized contribution of smart shunts is the potential for advanced control algorithms, such as weaning from shunt dependency and personalized control. With sensor-based control comes the opportunity to provide data to the physician on patient condition and shunt function, perhaps even by a smart phone. An often ignored but highly valuable contribution would be designs that correct the high failure rates of existing shunts. Despite the long history and increasing development activity in the past decade, patients are yet to see a commercialized smart shunt. Most smart shunt development focuses on concepts or on isolated technical features, but successful smart shunt designs will be a balance between technical feasibility, economic viability, and acceptable regulatory risk. Here, we present the status of this effort and a framework for understanding the challenges and opportunities that will guide introduction of smart shunts into patient care.
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Affiliation(s)
- Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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Lutz BR, Trinh P, Ball C, Fu E, Yager P. Two-dimensional paper networks: programmable fluidic disconnects for multi-step processes in shaped paper. Lab Chip 2011; 11:4274-8. [PMID: 22037591 PMCID: PMC4892121 DOI: 10.1039/c1lc20758j] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Most laboratory assays take advantage of multi-step protocols to achieve high performance, but conventional paper-based tests (e.g., lateral flow tests) are generally limited to assays that can be carried out in a single fluidic step. We have developed two-dimensional paper networks (2DPNs) that use materials from lateral flow tests but reconfigure them to enable programming of multi-step reagent delivery sequences. The 2DPN uses multiple converging fluid inlets to control the arrival time of each fluid to a detection zone or reaction zone, and it requires a method to disconnect each fluid source in a corresponding timed sequence. Here, we present a method that allows programmed disconnection of fluid sources required for multi-step delivery. A 2DPN with legs of different lengths is inserted into a shared buffer well, and the dropping fluid surface disconnects each leg at in a programmable sequence. This approach could enable multi-step laboratory assays to be converted into simple point-of-care devices that have high performance yet remain easy to use.
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Affiliation(s)
- Barry R Lutz
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA, USA.
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McKenzie KG, Lafleur LK, Lutz BR, Yager P. Rapid protein depletion from complex samples using a bead-based microfluidic device for the point of care. Lab Chip 2009; 9:3543-8. [PMID: 20024034 DOI: 10.1039/b913806d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Translation of sample preparation methods to point-of-care formats has remained a challenge. We present a plastic laminate microfluidic device for protein depletion from human plasma using ligand immobilized porous beads stored dry within a novel, pneumatically-driven mixer. The card design accelerated the protein depletion process from hours to minutes. Using immunoglobulin G as a model protein, we have successfully shown protein removal efficiency from spiked buffer between 70-80% and from diluted human plasma samples between 66-77%. Low non-specific binding of our downstream target ligand, immunoglobulin M, was observed with the spiked buffer and diluted human plasma samples. For future device optimization, the physical limitations to rapid protein removal on card were also explored. Bench-top experiments with improved mixing efficiency and a lower sample dilution factor achieved 99% IgG removal using the same amount of mixing time. This design can easily be adapted for depletion of other high abundance or interfering proteins by inclusion of other ligand immobilized beads.
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Affiliation(s)
- Katherine G McKenzie
- Department of Bioengineering, University of Washington, Box 355061, Foege N530J, Seattle, WA 98195-5061, USA.
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Abstract
Raman nanoparticle probes are an emerging new class of optical labels for interrogation of physiological and pathological processes in bioassays, cells, and tissues. Although their unique emission signatures are ideal for multiplexing, the full potential of these probes has not been realized because conventional analysis methods are inadequate. We report a novel spectral fitting method that exploits the entire spectral signature to quantitatively extract individual probe signals from multiplex spectra. We evaluate the method in a series of multiplex assays using unconjugated and antibody-conjugated composite organic-inorganic nanoparticles (COINs). Results show sensitive multiplex detection of small signals (<2% of total signal) and similar detection limits in corresponding 4-plex and singlet plate binding assays. In a triplex assay on formalin-fixed human prostate tissue, two antibody-conjugated COINs and a conventional fluorophore are used to image expression of prostate-specific antigen, cytokeratin-18, and DNA. The spectral analysis method effectively removes tissue autofluorescence and other unknown background, allowing accurate and reproducible imaging (area under ROC curve 0.89 +/- 0.03) at subcellular spatial resolution. In all assay systems, the error attributable to spectral analysis constitutes <or=2% of total signal. The spectral fitting method provides (1) quantification of signals from multiplex spectra with overlapping peaks, (2) robust spot-by-spot removal of unknown background, (3) the opportunity to quantitatively assess the analysis error, (4) elimination of operator bias, and (5) simple automation appropriate for high-throughput analysis. The simple implementation and universal applicability of this approach significantly expands the potential of Raman probes for quantitative in vivo and ex vivo multiplex analysis.
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Affiliation(s)
- Barry R. Lutz
- Biomedical/Life Sciences, Digital Health Group, Intel Corporation, SC3-41 2200 Mission College Boulevard, Santa Clara, California 95054
| | - Claire E. Dentinger
- Biomedical/Life Sciences, Digital Health Group, Intel Corporation, SC3-41 2200 Mission College Boulevard, Santa Clara, California 95054
| | - Lienchi N. Nguyen
- Biomedical/Life Sciences, Digital Health Group, Intel Corporation, SC3-41 2200 Mission College Boulevard, Santa Clara, California 95054
| | - Lei Sun
- Biomedical/Life Sciences, Digital Health Group, Intel Corporation, SC3-41 2200 Mission College Boulevard, Santa Clara, California 95054
| | - Jingwu Zhang
- Biomedical/Life Sciences, Digital Health Group, Intel Corporation, SC3-41 2200 Mission College Boulevard, Santa Clara, California 95054
| | - April N. Allen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, M5-A864, 1212 Aloha Street, Seattle, Washington 98109
| | - Selena Chan
- Biomedical/Life Sciences, Digital Health Group, Intel Corporation, SC3-41 2200 Mission College Boulevard, Santa Clara, California 95054
- Corresponding authors: ,
| | - Beatrice S. Knudsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, M5-A864, 1212 Aloha Street, Seattle, Washington 98109
- Corresponding authors: ,
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Abstract
A key need for dynamic single-cell measurements is the ability to gently position cells for repeated measurements without perturbing their behavior. We describe a new method that uses a gentle secondary flow to trap and suspend single cells, including motile cells, at predictable locations in 3-D. Trapped cells can be more dense or less dense than the surrounding medium. The cells are suspended without surface contact in one of four steady streaming eddies created by audible-frequency fluid oscillation (< or =1000 Hz) in a microchannel containing a single fixed cylinder (radius = 125 microm). Comparison of measured trap locations to computations of the eddy flow show that each trap is located near the eddy center, and the location is controlled via the oscillation frequency. We use the motile phytoplankton cell (Prorocentrum micans) to experimentally measure the trapping force, which is controlled via the oscillation amplitude. Trapping forces up to 30 pN are generated while exerting moderate shear stresses (shear stresses < or = 1.5 N/m2) on the trapped cell. The magnitude of this trapping force is comparable to that of optical tweezers or dielectrophoretic traps, without requiring an external field outside the physiological range for cells (the shear stresses are comparable to those found in arterial blood flow). The unique combination of predictable 3-D positioning, insensitivity to cell and medium properties, strong adjustable trapping forces, and a gentle fluid environment makes hydrodynamic tweezers a promising new option for noncontact trapping of single cells in suspension.
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Affiliation(s)
- Barry R Lutz
- Electrochemical Materials and Interfaces Laboratory, Department of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195-1750, USA
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Abstract
Well-mixed reaction volumes are often sought in engineered microchemical devices and can be an important feature of naturally occurring physicochemical processes such as pitting corrosion. Steady streaming eddies can serve as well-mixed, easily controlled microliter chemical reactors for characterizing homogeneous chemical reactions. Here, steady streaming eddies are produced by oscillating a liquid-filled cuvette around a stationary cylindrical electrode (radius 406 microm, length 1.6 cm) at audible frequencies (75 Hz). Oxidant (ferricyanide) electrochemically dosed at small rates (<or=30 nmol/s) from the cylindrical electrode accumulates to millimolar concentrations within the closed streamlines of each eddy, where it mixes and reacts with an antioxidant (vitamin C) present in the bulk solution. The composition in the eddy is controlled by varying the oxidant dosing rate and the bulk antioxidant concentration (<or=10 mM), as well as the cuvette oscillation amplitude. A simple algebraic mole balance is combined with Raman spectroscopy measurements of oxidant concentration in the eddy and bulk to determine the reaction rate law and homogeneous rate constant (45 +/- 9 M(-1) s(-1)) for the antioxidant properties of vitamin C against ferricyanide. Numerical solutions to the full Navier-Stokes equations and species continuity equations illustrate the distribution of species during the reaction and general limitations to the assumption of a well-mixed eddy.
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Affiliation(s)
- Barry R Lutz
- Electrochemical Materials and Interfaces Laboratory, Department of Chemical Engineering, Box 351750, University of Washington, Seattle, Washington 98195-1750, USA
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Abstract
Microfluidic devices create spatially defined, chemically controlled environments at microscopic dimensions. We demonstrate the formation and control of microscopic hydrodynamic and chemical environments by impinging a low-intensity acoustic oscillation on a cylindrical electrode. The interaction of small-amplitude (< or =203 microm), low-frequency (< or =515 Hz) fluid oscillations with a submillimeter cylinder creates four microscopic eddies that circulate adjacent to the cylinder. This steady flow is known as acoustic streaming. Because the steady circulation in the eddies has closed streamlines, reagent dosed from the electrode can escape the eddies only by slow molecular diffusion. As a result, reagent dosing rates of 10 nmol/s produce eddy concentrations as high as 8 mM, without a correspondingly large rise in bulk solution composition. Imaging Raman spectroscopy is used to visualize the eddy concentration distribution for various acoustic oscillation conditions, and point Raman spectra are used to quantify eddy compositions. These results, and corresponding numerical simulations, show that each eddy acts as a microchemical trap with size determined by acoustic frequency and the concentration tuned via reagent dosing rate and acoustic amplitude. Low-intensity acoustic streaming flows can serve as microfluidic elements without the need for microfabrication.
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Affiliation(s)
- Barry R Lutz
- Electrochemical Materials and Interfaces Laboratory, Department of Chemical Engineering, Box 351750, University of Washington, Seattle, WA 98195-1750, USA
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