1
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Pan CY, Kijamnajsuk P, Chen JJ. Portable loop-mediated isothermal amplification device with spectrometric detection for rapid pathogen identification. Anal Biochem 2024; 694:115615. [PMID: 39002745 DOI: 10.1016/j.ab.2024.115615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
With the rise in extreme weather due to global warming, coupled with globalization facilitating the spread of infectious diseases, there's a pressing need for portable testing platforms offering simplicity, low cost, and remote transmission, particularly beneficial in resource-limited and non-urban areas. We have developed a portable device using loop-mediated isothermal amplification (LAMP) with spectrometric detection to identify Salmonella Typhimurium DNA. The device utilizes the LinkIt 7697 microcontroller and a microspectrometer to capture and transmit spectral signals in real-time, allowing for improved monitoring and analysis of the reaction progress. We built a hand-held box containing a microspectrometer, thermoelectric cooler, ultraviolet LED, disposable reaction tube, and homemade thermal module, all powered by rechargeable batteries. Additionally, we conducted thorough experiments to ensure temperature accuracy within 1 °C under thermal control, developed a heating module with a LinkIt 7697 IoT development board to heat the DNA mixture to the reaction temperature within 3 min, and integrated foam insulation and a 3D-printed frame to enhance the device's thermal stability. We successfully demonstrated the amplification of Salmonella Typhimurium DNA with an impressive sensitivity of 2.83 × 10-4 ng/μL. A remote webpage interface allows for monitoring the temperature and fluorescence during the LAMP process, improving usability. This portable LAMP device with real-time detection offers a cost-effective solution for detecting Salmonella Typhimurium in food products. Its unique design and capabilities make it a promising tool for ensuring food safety.
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Affiliation(s)
- Chun Yu Pan
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan.
| | - Puchong Kijamnajsuk
- Department of Physics, Kasetsart University, 50 Ngamwongwan Rd, Lat Yao, Chatuchak, Bangkok, 10900, Thailand.
| | - Jyh Jian Chen
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan.
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2
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Sen A, Masetty M, Weerakoon S, Morris C, Yadav JS, Apewokin S, Trannguyen J, Broom M, Priye A. Paper-based loop-mediated isothermal amplification and CRISPR integrated platform for on-site nucleic acid testing of pathogens. Biosens Bioelectron 2024; 257:116292. [PMID: 38653014 DOI: 10.1016/j.bios.2024.116292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
We report the development and initial validation of a paper-based nucleic acid testing platform that integrates Loop-mediated isothermal amplification (LAMP) with clustered regularly interspaced short palindromic repeats (CRISPR) technology, referred to as PLACID (Paper-based LAMP-CRISPR Integrated Diagnostics). LAMP eliminates the need for thermal cycling, resulting in simplified instrumentation, and the CRISPR-associated protein (Cas 12a) system eliminates false positive signals from LAMP products, resulting in highly selective and sensitive assays. We optimized the assay to perform both amplification and detection entirely on paper, eliminating the need for complex fluid handling steps and lateral flow assay transfers. Additionally, we engineered a smartphone-operated system that includes a low-powered, non-contact IR heating chamber to actuate paper-based LAMP and CRISPR reactions and enable the detection of fluorescent signals from the paper. The platform demonstrates high specificity and sensitivity in detecting nucleic acid targets with a limit of detection of 50 copies/μL. We integrate an equipment-free sample preparation separation technology designed to streamline the preparation of crude samples prior to nucleic acid testing. The practical utility of our platform is demonstrated by the successful detection of spiked SARS-CoV-2 RNA fragments in saliva, E. Coli in soil, and pathogenic E. Coli in clinically fecal samples of infected patients. Furthermore, we demonstrate that the paper-based LAMP CRISPR chips employed in our assays possess a shelf life of several weeks, establishing them as viable candidates for on-site diagnostics.
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Affiliation(s)
- Anindita Sen
- DNAiTECH Ltd, Marlborough Research Center, 2650 State Highway 1, Grovetown, Blenheim, Marlborough, 7202, New Zealand
| | - Manaswini Masetty
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Sasanka Weerakoon
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Calum Morris
- DNAiTECH Ltd, Marlborough Research Center, 2650 State Highway 1, Grovetown, Blenheim, Marlborough, 7202, New Zealand
| | - Jagjit S Yadav
- Department of Environmental & Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Senu Apewokin
- Division of Infectious Diseases, College of Medicine, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Jennifer Trannguyen
- Division of Infectious Diseases, College of Medicine, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Murray Broom
- DNAiTECH Ltd, Marlborough Research Center, 2650 State Highway 1, Grovetown, Blenheim, Marlborough, 7202, New Zealand.
| | - Aashish Priye
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, 45221, USA; Digital Futures, University of Cincinnati, Cincinnati, OH, 45221, USA.
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3
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Chen Y, Zhu Y, Peng C, Wang X, Wu J, Chen H, Xu J. A Point-of-Care Nucleic Acid Quantification Method by Counting Light Spots Formed by LAMP Amplicons on a Paper Membrane. BIOSENSORS 2024; 14:139. [PMID: 38534246 DOI: 10.3390/bios14030139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
Nucleic acid quantification, allowing us to accurately know the copy number of target nucleic acids, is significant for diagnosis, food safety, agricultural production, and environmental protection. However, current digital quantification methods require expensive instruments or complicated microfluidic chips, making it difficult to popularize in the point-of-care detection. Paper is an inexpensive and readily available material. In this study, we propose a simple and cost-effective paper membrane-based digital loop-mediated isothermal amplification (LAMP) method for nucleic acid quantification. In the presence of DNA fluorescence dyes, the high background signals will cover up the amplicons-formed bright spots. To reduce the background fluorescence signals, a quencher-fluorophore duplex was introduced in LAMP primers to replace non-specific fluorescence dyes. After that, the amplicons-formed spots on the paper membrane can be observed; thus, the target DNA can be quantified by counting the spots. Take Vibrio parahaemolyticus DNA detection as an instance, a good linear relationship is obtained between the light spots and the copy numbers of DNA. The paper membrane-based digital LAMP detection can detect 100 copies target DNA per reaction within 30 min. Overall, the proposed nucleic acid quantification method has the advantages of a simple workflow, short sample-in and answer-out time, low cost, and high signal-to-noise, which is promising for application in resourced limited areas.
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Affiliation(s)
- Yanju Chen
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Zhu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Cheng Peng
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Huan Chen
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou 311215, China
| | - Junfeng Xu
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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4
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Bravo-González S, González-González E, Perales-Salinas V, Rodríguez-Sánchez IP, Ortiz-Castillo JE, Vargas-Martínez A, Perez-Gonzalez VH, Luna-Aguirre CM, Trujillo-de Santiago G, Alvarez MM. Self-Diagnosis of SARS-CoV-2 from Saliva Samples at Home: Isothermal Amplification Enabled by Do-It-Yourself Portable Incubators and Laminated Poly-ethyl Sulfonate Membranes. Diagnostics (Basel) 2024; 14:221. [PMID: 38275468 PMCID: PMC10814948 DOI: 10.3390/diagnostics14020221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024] Open
Abstract
COVID-19 made explicit the need for rethinking the way in which we conduct testing for epidemic emergencies. During the COVID-19 pandemic, the dependence on centralized lab facilities and resource-intensive methodologies (e.g., RT-qPCR methods) greatly limited the deployment of widespread testing efforts in many developed and underdeveloped countries. Here, we illustrate the development of a simple and portable diagnostic kit that enables self-diagnosis of COVID-19 at home from saliva samples. We describe the development of a do-it-yourself (DIY) incubator for Eppendorf tubes that can be used to conduct SARS-CoV-2 detection with competitive sensitivity and selectivity from saliva at home. In a proof-of-concept experiment, we assembled Eppendorf-tube incubators at our home shop, prepared a single-tube mix of reagents and LAMP primers in our lab, and deployed these COVID-19 detection kits using urban delivery systems (i.e., Rappifavor or Uber) to more than 15 different locations in Monterrey, México. This straightforward strategy enabled rapid and cost-effective at-home molecular diagnostics of SARS-CoV-2 from real saliva samples with a high sensitivity (100%) and high selectivity (87%).
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Affiliation(s)
- Sergio Bravo-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico
| | - Everardo González-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico
| | - Valeria Perales-Salinas
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico
| | - Iram Pablo Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, NL, Mexico;
- Alfa Medical Center, Guadalupe 67100, NL, Mexico
| | - Jose E. Ortiz-Castillo
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
| | - Adriana Vargas-Martínez
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
| | - Victor H. Perez-Gonzalez
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
| | - Claudia Maribel Luna-Aguirre
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (S.B.-G.); (E.G.-G.); (V.P.-S.); (C.M.L.-A.)
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico; (J.E.O.-C.); (A.V.-M.); (V.H.P.-G.)
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5
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Chen Y, Hu Y, Lu X. Polyethersulfone-Based Microfluidic Device Integrated with DNA Extraction on Paper and Recombinase Polymerase Amplification for the Detection of Salmonella enterica. ACS Sens 2023; 8:2331-2339. [PMID: 37228176 DOI: 10.1021/acssensors.3c00387] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Rising consumption, large-scale production, and widespread distribution have been accompanied by an increase in the number of Salmonella infections reported to implicate contaminated food products. We developed a portable origami microfluidic device that enabled rapid detection of S. enterica from sample preparation to end-point detection, including nucleic acid extraction on paper dipstick without pipetting, nucleic acid amplification using isothermal recombinase polymerase amplification (RPA), and lateral flow assay for results readout. We also explored the feasibility of the polyethersulfone (PES) membrane as a new reaction matrix against the widely used chromatography paper to optimize nucleic acid amplification. Nucleic acid amplification was achieved within 20 min and demonstrated 100% specificity to S. enterica. The limit of detection of this PES-based microfluidic device was 260 CFU/mL and equivalent to RPA reaction in tube. A chromatography paper-based microfluidic device was found 1-log less in sensitivity for Salmonella detection compared to the use of PES. This PES-based microfluidic device could detect S. enterica in lettuce, chicken breast, and milk at concentrations of 6 CFU/g, 9 CFU/g, and 58 CFU/mL, respectively, after 6 h enrichment. PES has shown high compatibility to isothermal nucleic acid amplification and great potential to be implemented as an integrated sample-to-answer microfluidic device for the detection of pathogens in various food commodities.
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Affiliation(s)
- Yunxuan Chen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yaxi Hu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Food Science Program, Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Food Science and Agricultural Chemistry, McGill University, 21111 Lakeshore Road,Sainte-Anne-de-Bellevue H9X 3V9 Quebec, Canada
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6
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Sritong N, Sala de Medeiros M, Basing LA, Linnes JC. Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens. LAB ON A CHIP 2023; 23:888-912. [PMID: 36688463 PMCID: PMC10028599 DOI: 10.1039/d2lc00554a] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | | | - Laud Anthony Basing
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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7
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Jawla J, Kumar RR, Mendiratta SK, Agarwal RK, Singh P, Saxena V, Kumari S, Kumar D. A novel paper based loop mediated isothermal amplification and lateral flow assay (LAMP‐LFA) for point‐of‐care detection of buffalo tissue origin in diverse foods. J Food Saf 2023. [DOI: 10.1111/jfs.13038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jyoti Jawla
- Division of Livestock Products Technology ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly India
| | - Rajiv Ranjan Kumar
- Division of Livestock Products Technology ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly India
| | - Sanjod Kumar Mendiratta
- Division of Livestock Products Technology ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly India
| | - Ravi Kant Agarwal
- Division of Livestock Products Technology ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly India
| | - Praveen Singh
- Division of Veterinary Biotechnology ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly India
| | - Vikas Saxena
- Center for Vascular & Inflammatory Diseases, School of Medicine University of Maryland Baltimore Maryland USA
| | - Sarita Kumari
- Division of Livestock Products Technology ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly India
| | - Dhananjay Kumar
- Division of Livestock Products Technology ICAR—Indian Veterinary Research Institute, Izatnagar Bareilly India
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8
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Lu X, Lin H, Feng X, Lui GC, Hsing IM. Disposable and low-cost pen-like sensor incorporating nucleic-acid amplification based lateral-flow assay for at-home tests of communicable pathogens. BIOSENSORS & BIOELECTRONICS: X 2022; 12:100248. [PMID: 36092541 PMCID: PMC9443926 DOI: 10.1016/j.biosx.2022.100248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/12/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Rapid at-home test is a good alternative to the gold standard quantitative polymerase chain reaction (qPCR) for early identification and management of infected individuals in pandemic. However, the currently available at-home rapid antigen kits and nucleic acid tests (NATs) are prone to false results. Although some CRISPR-mediated NATs enhanced accuracy, long turnaround time (ca. 1 h) and aerosol contamination due to additional open-lid reaction hinder its applicability for self-tests. Moreover, the accuracy of at-home NATs is also impacted by interference of sample matrix due to lack of sample purification. Here we report a Fast, Low-cost, Aerosol contamination-free and Sensitive molecular assay for at-Home tests of communicable pathogens (FLASH) incorporating oLAMP, a recently reported isothermal and target-specific NATs by our group, and a visible lateral-flow readout. The integrated platform enabled sample-to-result SARS-CoV-2 RNA detection in 20-30 min achieving a sensitivity of 0.5 copies/μL in a blinded experiment with a high accuracy comparable with the qPCR. Its prototype consists of two disposable pen-like instruments for single-step sample preparation and contamination-free NATs, respectively. The simplified workflow of the FLASH enabled detection to be readily conducted by untrained users for at-home tests. All in all, the FLASH prototype demonstrates itself to be a promising home-use assay platform for effective mitigation of the pandemic.
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Affiliation(s)
- Xiao Lu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Haosi Lin
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xianzhen Feng
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Grace Cy Lui
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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9
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Das D, Singh T, Ahmed I, Masetty M, Priye A. Effects of Relative Humidity and Paper Geometry on the Imbibition Dynamics and Reactions in Lateral Flow Assays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9863-9873. [PMID: 35913402 DOI: 10.1021/acs.langmuir.2c01017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lateral flow assays and paper microfluidics have the potential to replace benchtop instrumented medical diagnostic systems with instrument-free systems that rely on passive transport of liquid through micro-porous paper substrates. Predicting the imbibition dynamics of liquid through dry paper substrates is mostly modeled through the Lucas-Washburn (LW) equations. However, the LW framework assumes that the fluid front exhibits a sharp boundary between the dry and wet phases across the liquid imbibition interface. Additionally, the relative humidity in the environment results in moisture trapped within the pores of the paper substrates as the paper attains an equilibrium with the ambient air. Here, we apply a two-phase transport framework based on Brooks and Corey's model to capture imbibition dynamics on partially saturated paper substrates. The model is experimentally validated and is then used to predict the liquid-paper imbibition dynamics in simulated environments with 1-70% relative humidity. The model was also used to determine the saturation gradient of liquid along the imbibition interface of the paper substrate. Insights from these studies enabled us to determine the mechanism of the liquid transport in partially saturated porous paper substrates. The model also enabled us to evaluate the optimal paper shapes and relative humidity of the environment that maximize imbibition rates and minimize imbibition front broadening. Finally, we evaluate the effect of moisture content of paper on the rate of paper-based biochemical reaction by amplifying a sequence of the SARS-CoV-2 RNA target via reverse transcriptase loop-mediated isothermal amplification. Taken together, this study provides some important guidelines to academic and applied researchers working in point-of-care diagnostics to develop paper-based testing platforms that are capable of functioning in a robust manner across multiple environmental conditions.
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Affiliation(s)
- Debayan Das
- Department of Chemical Engineering, Shiv Nadar University, Uttar Pradesh 201314, India
| | - Tarun Singh
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Isteaque Ahmed
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Manaswini Masetty
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Aashish Priye
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio 45221, United States
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10
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A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma. Nat Biomed Eng 2022; 6:968-978. [PMID: 35941191 PMCID: PMC9361916 DOI: 10.1038/s41551-022-00919-w] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 07/01/2022] [Indexed: 12/19/2022]
Abstract
Rapid, accurate and frequent detection of the RNA of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and of serological host antibodies to the virus would facilitate the determination of the immune status of individuals who have Coronavirus disease 2019 (COVID-19), were previously infected by the virus, or were vaccinated against the disease. Here we describe the development and application of a 3D-printed lab-on-a-chip that concurrently detects, via multiplexed electrochemical outputs and within 2 h, SARS-CoV-2 RNA in saliva as well as anti-SARS-CoV-2 immunoglobulins in saliva spiked with blood plasma. The device automatedly extracts, concentrates and amplifies SARS-CoV-2 RNA from unprocessed saliva, and integrates the Cas12a-based enzymatic detection of SARS-CoV-2 RNA via isothermal nucleic acid amplification with a sandwich-based enzyme-linked immunosorbent assay on electrodes functionalized with the Spike S1, nucleocapsid and receptor-binding-domain antigens of SARS-CoV-2. Inexpensive microfluidic electrochemical sensors for performing multiplexed diagnostics at the point of care may facilitate the widespread monitoring of COVID-19 infection and immunity. A 3D-printed lab-on-a-chip allows for the concurrent rapid electrochemical detection of SARS-CoV-2 RNA in saliva and of anti-SARS-CoV-2 antibodies in saliva spiked with blood plasma.
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11
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Sullivan BP, Chou YS, Bender AT, Martin CD, Kaputa ZG, March H, Song M, Posner JD. Quantitative isothermal amplification on paper membranes using amplification nucleation site analysis. LAB ON A CHIP 2022; 22:2352-2363. [PMID: 35548880 PMCID: PMC9202034 DOI: 10.1039/d2lc00007e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and viral RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.
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Affiliation(s)
- Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Yu-Shan Chou
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Coleman D Martin
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
| | - Zoe G Kaputa
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Hugh March
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Minyung Song
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Stevens Way, Box 352600, Seattle, WA 98195, Washington, USA.
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
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12
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Automated liquid handling robot for rapid lateral flow assay development. Anal Bioanal Chem 2022; 414:2607-2618. [PMID: 35091761 PMCID: PMC8799445 DOI: 10.1007/s00216-022-03897-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/21/2021] [Accepted: 01/11/2022] [Indexed: 11/01/2022]
Abstract
AbstractThe lateral flow assay (LFA) is one of the most popular technologies on the point-of-care diagnostics market due to its low cost and ease of use, with applications ranging from pregnancy to environmental toxins to infectious disease. While the use of these tests is relatively straightforward, significant development time and effort are required to create tests that are both sensitive and specific. Workflows to guide the LFA development process exist but moving from target selection to an LFA that is ready for field testing can be labor intensive, resource heavy, and time consuming. To reduce the cost and the duration of the LFA development process, we introduce a novel development platform centered on the flexibility, speed, and throughput of an automated robotic liquid handling system. The system comprises LFA-specific hardware and software that enable large optimization experiments with discrete and continuous variables such as antibody pair selection or reagent concentration. Initial validation of the platform was demonstrated during development of a malaria LFA but was readily expanded to encompass development of SARS-CoV-2 and Mycobacterium tuberculosis LFAs. The validity of the platform, where optimization experiments are run directly on LFAs rather than in solution, was based on a direct comparison between the robotic system and a more traditional ELISA-like method. By minimizing hands-on time, maximizing experiment size, and enabling improved reproducibility, the robotic system improved the quality and quantity of LFA assay development efforts.
Graphical abstract
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13
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Sinha A, Basu M, Chandna P. Paper based microfluidics: A forecast toward the most affordable and rapid point-of-care devices. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:109-158. [PMID: 35033281 DOI: 10.1016/bs.pmbts.2021.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The microfluidic industry has evolved through years with acquired scientific knowledge from different, and already developed industries. Consequently, a wide range of materials like silicon from the electronic industry to all the way, silicone, from the chemical engineering industry, has been spotted to solve similar challenges. Although a typical microfluidic chip, fabricated from glass or polymer substrates offers definite benefits, however, paper-based microfluidic analytical devices (μPADs) possess numerous special benefits for practical implementation at a lower price. Owing to these features, in recent years, paper microfluidics has drawn immense interest from researchers in industry and academia alike. These devices have wider applications with advantages like lower cost, speedy detection, user-easiness, biocompatibility, sensitivity, and specificity etc. when compared to other microfluidic devices. Therefore, these sensitive but affordable devices fit themselves into point-of-care (POC) testing with features in demand like natural disposability, situational flexibility, and the capability to store and analyze the target at the point of requirement. Gradually, advancements in fabrication technologies, assay development techniques, and improved packaging capabilities, have contributed significantly to the real-time identification and health investigation through paper microfluidics; however, the growth has not been limited to the biomedical field; industries like electronics, energy storage and many more have expanded substantially. Here, we represent an overall state of the paper-based microfluidic technology by covering the fundamentals, working principles, different fabrication procedures, applications for various needs and then to make things more practical, the real-life scenario and practical challenges involved in launching a device into the market have been revealed. To conclude, recent contribution of μPADs in the 2020 pandemic and potential future possibilities have been reviewed.
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14
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Sullivan BP, Chou YS, Bender AT, Martin CD, Kaputa ZG, March H, Song M, Posner JD. Quantitative Isothermal Amplification on Paper Membranes using Amplification Nucleation Site Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.11.475898. [PMID: 35043115 PMCID: PMC8764744 DOI: 10.1101/2022.01.11.475898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantitative nucleic acid amplification tests (qNAATs) are critical in treating infectious diseases, such as in HIV viral load monitoring or SARS-CoV-2 testing, in which viral load indicates viral suppression or infectivity. Quantitative PCR is the gold standard tool for qNAATs; however, there is a need to develop point-of-care (POC) qNAATs to manage infectious diseases in outpatient clinics, low- and middle-income countries, and the home. Isothermal amplification methods are an emerging tool for POC NAATs as an alternative to traditional PCR-based workflows. Previous works have focused on relating isothermal amplification bulk fluorescence signals to input copies of target nucleic acids for sample quantification with limited success. In this work, we show that recombinase polymerase amplification (RPA) reactions on paper membranes exhibit discrete fluorescent amplification nucleation sites. We demonstrate that the number of nucleation sites can be used to quantify HIV-1 DNA and RNA in less than 20 minutes. An image-analysis algorithm quantifies nucleation sites and determines the input nucleic acid copies in the range of 67-3,000 copies per reaction. We demonstrate a mobile phone-based system for image capture and onboard processing, illustrating that this method may be used at the point-of-care for qNAATs with minimal instrumentation.
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15
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Zamani M, Furst AL, Klapperich CM. Strategies for Engineering Affordable Technologies for Point-of-Care Diagnostics of Infectious Diseases. Acc Chem Res 2021; 54:3772-3779. [PMID: 34612619 PMCID: PMC8996141 DOI: 10.1021/acs.accounts.1c00434] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Disease prevalence is highest in low-resource settings (LRS) due to the lack of funds, infrastructure, and personnel required to carry out laboratory-based molecular tests. In high-resource settings, gold-standard molecular tests for diseases consist of nucleic acid amplification tests (NAATs) due to their excellent sensitivity and specificity. These tests require the extraction, amplification, and detection of nucleic acids from clinical samples. In high-resource settings, all three of these steps require highly specialized, costly, and onerous equipment that cannot be used in LRS. Nucleic acid extraction involves multiple centrifugation steps. Amplification consists of the polymerase chain reaction (PCR), which requires thermal cyclers. The detection of amplified DNA is typically done with specialized thermal cyclers that are capable of fluorescence detection. Traditional methods used to extract, amplify, and detect nucleic acids cannot be used outside of a laboratory in LRS. Thus, there is a need for affordable point-of-care devices to ease the high burden of disease in LRS.The past decade of work on paper-based fluidic devices has resulted in the invention of many paper-based biosensors for disease detection as well as isothermal amplification techniques that replace PCR. However, a challenge still remains in detecting pathogenic biomarkers from complex human samples without specialized laboratory equipment. Our research has focused on the development of affordable technologies to extract and detect nucleic acids in clinical samples with minimal equipment. Here we describe methods for the paper-based extraction, amplification, and detection of nucleic acids. This Account provides an overview of our latest technologies developed to detect an array of diseases in low-resource settings. We focus on detecting nucleic acids of H1N1, human papillomavirus (HPV), Neisseria gonorrheae (NG), Chlamydia trachomatis (CT), Trichomonas vaginalis (TV), and malaria from a variety of clinical sample types. H1N1 RNA was extracted from nasopharyngeal swabs; HPV, NG, and CT DNA were extracted from either cervical, urethral, or vaginal swabs; TV DNA was extracted from urine; and malaria DNA was extracted from whole blood. Different sample types necessitate different nucleic extraction protocols; we provide guidelines for assay design based on the clinical sample type used. We compare the pros and cons of different isothermal amplification techniques, namely, helicase-dependent amplification (HDA), loop-mediated isothermal amplification (LAMP), and a novel isothermal amplification technique that we developed: isothermal-identical multirepeat sequences (iso-IMRS). Finally, we compare various detection mechanisms, including lateral-flow and electrochemical readouts. Electrochemical readouts frequently employ gold electrodes due to strong gold-thiol coupling. However, the high cost of gold precludes their use in LRS. We discuss our development of novel gold leaf electrodes that can be made without specialized equipment for a fraction of the cost of commercially available gold electrodes.
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Affiliation(s)
- Marjon Zamani
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ariel L Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Catherine M Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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16
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Jawla J, Kumar RR, Mendiratta S, Agarwal R, Singh P, Saxena V, Kumari S, Boby N, Kumar D, Rana P. On-site paper-based Loop-Mediated Isothermal Amplification coupled Lateral Flow Assay for pig tissue identification targeting mitochondrial CO I gene. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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de Puig H, Lee RA, Najjar D, Tan X, Soeknsen LR, Angenent-Mari NM, Donghia NM, Weckman NE, Ory A, Ng CF, Nguyen PQ, Mao AS, Ferrante TC, Lansberry G, Sallum H, Niemi J, Collins JJ. Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants. SCIENCE ADVANCES 2021; 7:7/32/eabh2944. [PMID: 34362739 PMCID: PMC8346217 DOI: 10.1126/sciadv.abh2944] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/17/2021] [Indexed: 05/04/2023]
Abstract
The COVID-19 pandemic highlights the need for diagnostics that can be rapidly adapted and deployed in a variety of settings. Several SARS-CoV-2 variants have shown worrisome effects on vaccine and treatment efficacy, but no current point-of-care (POC) testing modality allows their specific identification. We have developed miSHERLOCK, a low-cost, CRISPR-based POC diagnostic platform that takes unprocessed patient saliva; extracts, purifies, and concentrates viral RNA; performs amplification and detection reactions; and provides fluorescent visual output with only three user actions and 1 hour from sample input to answer out. miSHERLOCK achieves highly sensitive multiplexed detection of SARS-CoV-2 and mutations associated with variants B.1.1.7, B.1.351, and P.1. Our modular system enables easy exchange of assays to address diverse user needs and can be rapidly reconfigured to detect different viruses and variants of concern. An adjunctive smartphone application enables output quantification, automated interpretation, and the possibility of remote, distributed result reporting.
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Affiliation(s)
- Helena de Puig
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rose A Lee
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Devora Najjar
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xiao Tan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Luis R Soeknsen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nicolaas M Angenent-Mari
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nina M Donghia
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Nicole E Weckman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Audrey Ory
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- College of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Carlos F Ng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Peter Q Nguyen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Angelo S Mao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thomas C Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Geoffrey Lansberry
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Hani Sallum
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - James Niemi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- College of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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18
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Gürel-Gökmen B, Taslak HD, Özcan O, İpar N, Tunali-Akbay T. Polycaprolactone/silk fibroin electrospun nanofibers-based lateral flow test strip for quick and facile determination of bisphenol A in breast milk. J Biomed Mater Res B Appl Biomater 2021; 109:1455-1464. [PMID: 33501724 DOI: 10.1002/jbm.b.34805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 12/13/2020] [Accepted: 01/09/2021] [Indexed: 01/06/2023]
Abstract
This study aimed to develop a sensitive lateral flow test strip for the detection of bisphenol A (BPA) in breast milk. Conventional nitrocellulose test membrane was coated with the coaxial nanofiber, consisting of the inner polycaprolactone (PCL) and the outer PCL/silk fibroin (SF) mixture, to decrease the flow rate of the breast milk in the lateral flow assay (LFA). The nanofiber was prepared by using coaxial electrospinning, and BPA antibody was immobilized physically to the nanofiber. This nanofiber was used as a test membrane in the LFA. Color changes on the test membrane were evaluated as the signal intensity of the BPA. Breast milk creates a background on surfaces due to its structural properties. This background was detected by comparing the signal intensity with the signal intensity of water. The higher signal intensity was found in water samples when compared to breast milk samples. Although the detection limit is 2 ng/ml in both coaxial PCL/SF nanofiber and nitrocellulose (NC) test membranes, the color intensity increased with the increasing BPA concentration in the coaxial PCL/SF nanofiber. As a new dimension, the coaxial PCL/SF nanofiber provided higher color intensity than the NC membrane. In conclusion, a sensitive onsite method was developed for the detection of BPA in breast milk by using new coaxial PCL/SF nanofiber as a test membrane in LFA.
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Affiliation(s)
- Begüm Gürel-Gökmen
- Faculty of Dentistry, Department of Biochemistry, Marmara University, İstanbul, Turkey
| | - Hava Dudu Taslak
- Faculty of Dentistry, Department of Biochemistry, Marmara University, İstanbul, Turkey
| | - Ozan Özcan
- Faculty of Dentistry, Department of Biochemistry, Marmara University, İstanbul, Turkey
| | - Necla İpar
- Department of Pediatrics, Koc University Hospital, İstanbul, Turkey
| | - Tuğba Tunali-Akbay
- Faculty of Dentistry, Department of Biochemistry, Marmara University, İstanbul, Turkey
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19
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Jawla J, Kumar RR, Mendiratta SK, Agarwal RK, Kumari S, Saxena V, Kumar D, Singh P, Boby N, Rana P. Paper-based loop-mediated isothermal amplification and lateral flow (LAMP-LF) assay for identification of tissues of cattle origin. Anal Chim Acta 2021; 1150:338220. [PMID: 33583554 DOI: 10.1016/j.aca.2021.338220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/15/2021] [Indexed: 11/24/2022]
Abstract
The present study was made with the objectives of development and standardization of cattle specific paper-based loop-mediated isothermal amplification cum lateral flow assay (LAMP-LFA), as a Point-of-care test (POCT) for identification of tissue of cattle origin. The components of standardized LAMP reaction utilizing cattle specific primer sets were lyophilized over paper buttons, identified best as the carrier of LAMP reagents. Based on probable LAMP amplicon, a pair of probes was designed, tagged and its hybridization with the amplified product of paper LAMP reaction was optimized. The components of lateral flow assay for detection of probe hybridized LAMP products were standardized. Analysis of successful amplification was made by using HNB dye, LAMP-LFA strip, and also by the typical ladder-like pattern on gel electrophoresis. The assay was found highly specific for cattle with an analytical sensitivity of 0.1 pg of absolute DNA. Laboratory validation carried out on samples from different individuals of cattle, coded samples, binary meat admixture, and heat-processed cattle tissues substantiated the accuracy of the assay. Comparison with pre-standardized species-specific PCR assay taken as gold standards revealed 100% conformity. The field utility of the developed assay was further established by its compatibility with the commercial kit eliminating the lengthy DNA extraction step and storage stability of LAMP reagent carrier buttons for 4 months under refrigeration. Thus, the developed assay capable of the result within 3 h in resource-limited settings can be used as POCT for identification of tissue of cattle origin.
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Affiliation(s)
- Jyoti Jawla
- Department of Livestock Products Technology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India.
| | - Rajiv Ranjan Kumar
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, India.
| | - S K Mendiratta
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, India.
| | - R K Agarwal
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, India.
| | - Sarita Kumari
- Department of Livestock Products Technology, PGIVER, RAJUVAS, Jaipur, India.
| | - Vikas Saxena
- Center for Vascular & Inflammatory Diseases, School of Medicine, University of Maryland, Baltimore, MD, USA.
| | - Dhananjay Kumar
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, India.
| | - Praveen Singh
- I/C CIF Bioengineering, Division of Vet Biotechnology, Indian Veterinary Research Institute, Izatnagar, India.
| | - Nongthombam Boby
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, India.
| | - Preeti Rana
- Department of Livestock Products Technology, CVASc, DUVASU, Mathura, India.
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20
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Paper-Based Nucleic Acid Detection for Point-of-Care Diagnostics. Bioanalysis 2021. [DOI: 10.1007/978-981-15-8723-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Rui X, Song S, Wang W, Zhou J. Applications of electrowetting-on-dielectric (EWOD) technology for droplet digital PCR. BIOMICROFLUIDICS 2020; 14:061503. [PMID: 33312327 PMCID: PMC7719047 DOI: 10.1063/5.0021177] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/24/2020] [Indexed: 05/25/2023]
Abstract
Digital microfluidics is an elegant technique based on single droplets for the design, composition, and manipulation of microfluidic systems. In digital microfluidics, especially in the electrowetting on dielectric (EWOD) system, each droplet acts as an independent reactor, which enables a wide range of multiple parallel biological and chemical reactions at the microscale. EWOD digital microfluidics reduces reagent and energy consumption, accelerates analysis, enables point-of-care diagnostic, simplifies integration with sensors, etc. Such a digital microfluidic system is especially relevant for droplet digital PCR (ddPCR), thanks to its nanoliter droplets and well-controlled volume distribution. At low DNA concentration, these small volumes allow less than one DNA strand per droplet on average (limited dilution) so that after a fixed number of PCR cycles (endpoint PCR), only the DNA in droplets containing the sequence of interest has been amplified and can be detected by fluorescence to yield an accurate count of the sequences of interest using statistical models. Focusing on ddPCR, this article summarizes the latest development and research on EWOD technology for droplet PCR over the last decade.
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Affiliation(s)
| | | | | | - Jia Zhou
- Author to whom correspondence should be addressed:
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22
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Suea-Ngam A, Bezinge L, Mateescu B, Howes PD, deMello AJ, Richards DA. Enzyme-Assisted Nucleic Acid Detection for Infectious Disease Diagnostics: Moving toward the Point-of-Care. ACS Sens 2020; 5:2701-2723. [PMID: 32838523 PMCID: PMC7485284 DOI: 10.1021/acssensors.0c01488] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/25/2020] [Indexed: 02/08/2023]
Abstract
Driven by complex and interconnected factors, including population growth, climate change, and geopolitics, infectious diseases represent one of the greatest healthcare challenges of the 21st century. Diagnostic technologies are the first line of defense in the fight against infectious disease, providing critical information to inform epidemiological models, track diseases, decide treatment choices, and ultimately prevent epidemics. The diagnosis of infectious disease at the genomic level using nucleic acid disease biomarkers has proven to be the most effective approach to date. Such methods rely heavily on enzymes to specifically amplify or detect nucleic acids in complex samples, and significant effort has been exerted to harness the power of enzymes for in vitro nucleic acid diagnostics. Unfortunately, significant challenges limit the potential of enzyme-assisted nucleic acid diagnostics, particularly when translating diagnostic technologies from the lab toward the point-of-use or point-of-care. Herein, we discuss the current state of the field and highlight cross-disciplinary efforts to solve the challenges associated with the successful deployment of this important class of diagnostics at or near the point-of-care.
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Affiliation(s)
- Akkapol Suea-Ngam
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Léonard Bezinge
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Bogdan Mateescu
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
- Brain Research Institute,
Medical Faculty of the University of
Zürich, Winterthurerstrasse 190, 8057
Zürich, Switzerland
| | - Philip D. Howes
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Andrew J. deMello
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Daniel A. Richards
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
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23
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Dixon C, Lamanna J, Wheeler AR. Direct loading of blood for plasma separation and diagnostic assays on a digital microfluidic device. LAB ON A CHIP 2020; 20:1845-1855. [PMID: 32338260 DOI: 10.1039/d0lc00302f] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Finger-stick blood sampling is convenient for point of care diagnostics, but whole blood samples are problematic for many assays because of severe matrix effects associated with blood cells and cell debris. We introduce a new digital microfluidic (DMF) diagnostic platform with integrated porous membranes for blood-plasma separation from finger-stick blood volumes, capable of performing complex, multi-step, diagnostic assays. Importantly, the samples can be directly loaded onto the device by a finger "dab" for user-friendly operation. We characterize the platform by comparison to plasma generated via the "gold standard" centrifugation technique, and demonstrate a 21-step rubella virus (RV) IgG immunoassay yielding a detection limit of 1.9 IU mL-1, below the diagnostic cut-off. We propose that this work represents a critical next step in DMF based portable diagnostic assays-allowing the analysis of whole blood samples without pre-processing.
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Affiliation(s)
- Christopher Dixon
- Department of Chemistry, University of Toronto, 80. St. George Street, Toronto, Ontario M5S 3H6, Canada.
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24
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Naik P, Jaitpal S, Paul D. The Resurgence of Paperfluidics: A new technology for cell, DNA, and blood analysis. IEEE NANOTECHNOLOGY MAGAZINE 2020. [DOI: 10.1109/mnano.2020.2966063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Yee EH, Sikes HD. Polymerization-Based Amplification for Target-Specific Colorimetric Detection of Amplified Mycobacterium tuberculosis DNA on Cellulose. ACS Sens 2020; 5:308-312. [PMID: 31970983 DOI: 10.1021/acssensors.9b02424] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an appealing method for low-cost, point-of-care nucleic acid diagnostic assays due to high sensitivity, minimal equipment requirements, and compatibility with user-friendly colorimetric detection methods. The enhanced sensitivity LAMP offers comes with vulnerability to cross-contamination, where negative samples are exposed to minute amounts of nucleic acids from positive samples. These amounts are insignificant in less sensitive amplification methods, but visible when LAMP is paired with common colorimetric methods. Here, we examined the use of eosin photopolymerization, a tunable reaction, for colorimetric detection of LAMP products to reduce this false positive risk. Using eosin and biotin end-labeled primers, we successfully amplified target regions of the Mycobacterium tuberculosis (MTB) genome using PCR and LAMP, captured amplicons on streptavidin-coated cellulose, and detected DNA targets via eosin photopolymerization, producing a bright pink color only if MTB DNA was present in the sample. Consistent with previous reports, the LAMP-based method exhibited high background signal, but tuning the illumination time for the photopolymerization reaction allowed readouts from samples with no added MTB DNA to remain blank and visually distinct from pink positives. This method yielded limits of detection of 30 and 300 copies/μL for LAMP and PCR amplification, respectively. When confronted with boiled MTB culture samples, this method gave clear positive readouts, compared to negligible signal from other Mycobacterium boiled culture samples. This new method of LAMP colorimetric detection has the potential to increase the utility of LAMP as a nucleic acid assay technique by mitigating sensitivity to cross-contamination.
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Affiliation(s)
| | - Hadley D. Sikes
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
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Obande GA, Banga Singh KK. Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections. Infect Drug Resist 2020; 13:455-483. [PMID: 32104017 PMCID: PMC7024801 DOI: 10.2147/idr.s217571] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.
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Affiliation(s)
- Godwin Attah Obande
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Microbiology, Faculty of Science, Federal University Lafia, Lafia, Nasarawa State, Nigeria
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
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Phillips EA, Moehling TJ, Ejendal KFK, Hoilett OS, Byers KM, Basing LA, Jankowski LA, Bennett JB, Lin LK, Stanciu LA, Linnes JC. Microfluidic rapid and autonomous analytical device (microRAAD) to detect HIV from whole blood samples. LAB ON A CHIP 2019; 19:3375-3386. [PMID: 31539001 PMCID: PMC7384476 DOI: 10.1039/c9lc00506d] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
While identifying acute HIV infection is critical to providing prompt treatment to HIV-positive individuals and preventing transmission, existing laboratory-based testing methods are too complex to perform at the point of care. Specifically, molecular techniques can detect HIV RNA within 8-10 days of transmission but require laboratory infrastructure for cold-chain reagent storage and extensive sample preparation performed by trained personnel. Here, we demonstrate our point-of-care microfluidic rapid and autonomous analysis device (microRAAD) that automatically detects HIV RNA from whole blood. Inside microRAAD, we incorporate vitrified amplification reagents, thermally-actuated valves for fluidic control, and a temperature control circuit for low-power heating. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) products are visualized using a lateral flow immunoassay (LFIA), resulting in an assay limit of detection of 100 HIV-1 RNA copies when performed as a standard tube reaction. Even after three weeks of room-temperature reagent storage, microRAAD automatically isolates the virus from whole blood, amplifies HIV-1 RNA, and transports amplification products to the internal LFIA, detecting as few as 3 × 105 HIV-1 viral particles, or 2.3 × 107 virus copies per mL of whole blood, within 90 minutes. This integrated microRAAD is a low-cost and portable platform to enable automated detection of HIV and other pathogens at the point of care.
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Affiliation(s)
- Elizabeth A Phillips
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA.
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Yin J, Suo Y, Zou Z, Sun J, Zhang S, Wang B, Xu Y, Darland D, Zhao JX, Mu Y. Integrated microfluidic systems with sample preparation and nucleic acid amplification. LAB ON A CHIP 2019; 19:2769-2785. [PMID: 31365009 PMCID: PMC8876602 DOI: 10.1039/c9lc00389d] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Rapid, efficient and accurate nucleic acid molecule detection is important in the screening of diseases and pathogens, yet remains a limiting factor at point of care (POC) treatment. Microfluidic systems are characterized by fast, integrated, miniaturized features which provide an effective platform for qualitative and quantitative detection of nucleic acid molecules. The nucleic acid detection process mainly includes sample preparation and target molecule amplification. Given the advancements in theoretical research and technological innovations to date, nucleic acid extraction and amplification integrated with microfluidic systems has advanced rapidly. The primary goal of this review is to outline current approaches used for nucleic acid detection in the context of microfluidic systems. The secondary goal is to identify new approaches that will help shape future trends at the intersection of nucleic acid detection and microfluidics, particularly with regard to increasing disease and pathogen detection for improved diagnosis and treatment.
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Affiliation(s)
- Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanjie Suo
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Zheyu Zou
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Jingjing Sun
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Shan Zhang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Beng Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009 China and Institute of Translational Medicine, Zhejiang University, Hangzhou, 310029 China
| | - Yawei Xu
- College of Biological and Pharmaceutical Engineering, Jilin Agricultural Science and Technology University, Jilin, 132000 China
| | - Diane Darland
- Department of Biology, University of North Dakota, USA.
| | | | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
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Ammanath G, Yeasmin S, Srinivasulu Y, Vats M, Cheema JA, Nabilah F, Srivastava R, Yildiz UH, Alagappan P, Liedberg B. Flow-through colorimetric assay for detection of nucleic acids in plasma. Anal Chim Acta 2019; 1066:102-111. [DOI: 10.1016/j.aca.2019.03.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/13/2019] [Accepted: 03/17/2019] [Indexed: 01/04/2023]
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30
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Liu L, Yang D, Liu G. Signal amplification strategies for paper-based analytical devices. Biosens Bioelectron 2019; 136:60-75. [DOI: 10.1016/j.bios.2019.04.043] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/15/2019] [Accepted: 04/21/2019] [Indexed: 12/26/2022]
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Paper-based microfluidics for DNA diagnostics of malaria in low resource underserved rural communities. Proc Natl Acad Sci U S A 2019; 116:4834-4842. [PMID: 30782834 PMCID: PMC6421471 DOI: 10.1073/pnas.1812296116] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Populations living in remote rural communities would benefit from rapid, highly sensitive molecular, DNA-based diagnostics to inform the correct and timely treatment of infectious diseases. Such information is also becoming increasingly relevant in global efforts for disease elimination, where the testing of asymptomatic patients is now seen as being important for the identification of disease reservoirs. However, healthcare workers face practical and logistical problems in the implementation of such tests, which often involve complex instrumentation and centralized laboratories. Here we describe innovations in paper microfluidics that enable low-cost, multiplexed DNA-based diagnostics for malaria, delivered, in a first-in-human study, in schools in rural Uganda. Rapid, low-cost, species-specific diagnosis, based upon DNA testing, is becoming important in the treatment of patients with infectious diseases. Here, we demonstrate an innovation that uses origami to enable multiplexed, sensitive assays that rival polymerase chain reactions (PCR) laboratory assays and provide high-quality, fast precision diagnostics for malaria. The paper-based microfluidic technology proposed here combines vertical flow sample-processing steps, including paper folding for whole-blood sample preparation, with an isothermal amplification and a lateral flow detection, incorporating a simple visualization system. Studies were performed in village schools in Uganda with individual diagnoses being completed in <50 min (faster than the standard laboratory-based PCR). The tests, which enabled the diagnosis of malaria species in patients from a finger prick of whole blood, were both highly sensitive and specific, detecting malaria in 98% of infected individuals in a double-blind first-in-human study. Our method was more sensitive than other field-based, benchmark techniques, including optical microscopy and industry standard rapid immunodiagnostic tests, both performed by experienced local healthcare teams (which detected malaria in 86% and 83% of cases, respectively). All assays were independently validated using a real-time double-blinded reference PCR assay. We not only demonstrate that advanced, low-cost DNA-based sensors can be implemented in underserved communities at the point of need but also highlight the challenges associated with developing and implementing new diagnostic technologies in the field, without access to laboratories or infrastructure.
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Markwalter C, Kantor AG, Moore CP, Richardson KA, Wright DW. Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics. Chem Rev 2019; 119:1456-1518. [PMID: 30511833 PMCID: PMC6348445 DOI: 10.1021/acs.chemrev.8b00136] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Indexed: 12/12/2022]
Abstract
Infectious diseases claim millions of lives each year. Robust and accurate diagnostics are essential tools for identifying those who are at risk and in need of treatment in low-resource settings. Inorganic complexes and metal-based nanomaterials continue to drive the development of diagnostic platforms and strategies that enable infectious disease detection in low-resource settings. In this review, we highlight works from the past 20 years in which inorganic chemistry and nanotechnology were implemented in each of the core components that make up a diagnostic test. First, we present how inorganic biomarkers and their properties are leveraged for infectious disease detection. In the following section, we detail metal-based technologies that have been employed for sample preparation and biomarker isolation from sample matrices. We then describe how inorganic- and nanomaterial-based probes have been utilized in point-of-care diagnostics for signal generation. The following section discusses instrumentation for signal readout in resource-limited settings. Next, we highlight the detection of nucleic acids at the point of care as an emerging application of inorganic chemistry. Lastly, we consider the challenges that remain for translation of the aforementioned diagnostic platforms to low-resource settings.
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Affiliation(s)
| | | | | | | | - David W. Wright
- Department of Chemistry, Vanderbilt
University, Nashville, Tennessee 37235, United States
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Nanayakkara IA, White IM. Demonstration of a quantitative triplex LAMP assay with an improved probe-based readout for the detection of MRSA. Analyst 2019; 144:3878-3885. [DOI: 10.1039/c9an00671k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A LAMP assay that simultaneously detects three MRSA genes within a single sample using a quantitative and real-time readout is designed and demonstrated.
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Affiliation(s)
| | - Ian M. White
- Fischell Department of Bioengineering
- University of Maryland
- College Park
- USA
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34
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Cheung SF, Yee MF, Le NK, Wu BM, Kamei DT. A one-pot, isothermal DNA sample preparation and amplification platform utilizing aqueous two-phase systems. Anal Bioanal Chem 2018; 410:5255-5263. [PMID: 29947898 DOI: 10.1007/s00216-018-1178-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/21/2018] [Accepted: 05/30/2018] [Indexed: 12/18/2022]
Abstract
Infectious diseases remain one of the major causes of death worldwide in developing countries. While screening via conventional polymerase chain reaction (PCR) is the gold standard in laboratory testing, its limited applications at the point-of-care have prompted the development of more portable nucleic acid detection systems. These include isothermal DNA amplification techniques, which are less equipment-intensive than PCR. Unfortunately, these techniques still require extensive sample preparation, limiting user accessibility. In this study, we introduce a novel system that combines thermophilic helicase-dependent amplification (tHDA) with a Triton X-100 micellar aqueous two-phase system (ATPS) to achieve cell lysis, lysate processing, and enhanced nucleic acid amplification in a simple, one-step process. The combined one-pot system was able to amplify and detect a target gene from whole-cell samples containing as low as 102 cfu/mL, and is the first known application of ATPSs to isothermal DNA amplification. This system's ease-of-use and sensitivity underlie its potential as a point-of-care diagnostic platform to detect for infectious diseases. Graphical abstract ᅟ.
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Affiliation(s)
- Sherine F Cheung
- Department of Bioengineering, University of California, 5121 Engineering V, 420 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Matthew F Yee
- Department of Bioengineering, University of California, 5121 Engineering V, 420 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Nguyen K Le
- Department of Bioengineering, University of California, 5121 Engineering V, 420 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Benjamin M Wu
- Department of Bioengineering, University of California, 5121 Engineering V, 420 Westwood Plaza, Los Angeles, CA, 90095, USA.,Division of Advanced Prosthodontics & Weintraub Center for Reconstructive Biotechnology, UCLA School of Dentistry, Los Angeles, CA, 90095, USA
| | - Daniel T Kamei
- Department of Bioengineering, University of California, 5121 Engineering V, 420 Westwood Plaza, Los Angeles, CA, 90095, USA.
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Toley BJ, Das D, Ganar KA, Kaur N, Meena M, Rath D, Sathishkumar N, Soni S. Multidimensional Paper Networks: A New Generation of Low-Cost Pump-Free Microfluidic Devices. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0077-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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36
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Wang H, Deng J, Tang YW. Profile of the Alere i Influenza A & B assay: a pioneering molecular point-of-care test. Expert Rev Mol Diagn 2018; 18:403-409. [PMID: 29688086 PMCID: PMC6153442 DOI: 10.1080/14737159.2018.1466703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The Alere i Influenza A & B assay incorporates the Nicking Enzyme Amplification Reaction technique on the Alere i instrument to detect and differentiate influenza virus (Flu) A and B nucleic acids in specific specimens. Areas covered: The Alere i Influenza A & B assay was cleared by the US Food and Drug Administration for use with nasal swabs (NS) and nasopharyngeal swabs, either directly or in viral transport medium. Notably, direct use on NS was the first ever CLIA-waived nucleic acid-based test. Previously published evaluations have reported sensitivities and specificities of 55.2-100% and 62.5-100% for Flu A and 45.2-100% and 53.6-100% for Flu B, respectively. Expert commentary: The Alere i Influenza A & B assay provides a rapid and simple platform for detection and differentiation of Flu A and B. Efforts are expected to further improve sensitivity and user-friendliness for effective and widespread use in the true point-of-care setting.
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Affiliation(s)
- Hongmei Wang
- Division of Infectious Diseases, Shenzhen Children Hospital, Shenzhen, China
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Jikui Deng
- Division of Infectious Diseases, Shenzhen Children Hospital, Shenzhen, China
| | - Yi-Wei Tang
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, USA
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37
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Horst AL, Rosenbohm JM, Kolluri N, Hardick J, Gaydos CA, Cabodi M, Klapperich CM, Linnes JC. A paperfluidic platform to detect Neisseria gonorrhoeae in clinical samples. Biomed Microdevices 2018; 20:35. [PMID: 29644437 PMCID: PMC6154386 DOI: 10.1007/s10544-018-0280-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Globally, the microbe Neisseria gonorrhoeae (NG) causes 106 million newly documented sexually transmitted infections each year. Once appropriately diagnosed, NG infections can be readily treated with antibiotics, but high-risk patients often do not return to the clinic for treatment if results are not provided at the point of care. A rapid, sensitive molecular diagnostic would help increase NG treatment and reduce the prevalence of this sexually transmitted disease. Here, we report on the design and development of a rapid, highly sensitive, paperfluidic device for point-of-care diagnosis of NG. The device integrates patient swab sample lysis, nucleic acid extraction, thermophilic helicase-dependent amplification (tHDA), an internal amplification control (NGIC), and visual lateral flow detection within an 80 min run time. Limits of NG detection for the NG/NGIC multiplex tHDA assay were determined within the device, and clinical performance was validated retroactively against qPCR-quantified patient samples in a proof-of-concept study. This paperfluidic diagnostic has a clinically relevant limit of detection of 500 NG cells per device with analytical sensitivity down to 10 NG cells per device. In triplicate testing of 40 total urethral and vaginal swab samples, the device had 95% overall sensitivity and 100% specificity, approaching current laboratory-based molecular NG diagnostics. This diagnostic platform could increase access to accurate NG diagnoses to those most in need.
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Affiliation(s)
- Audrey L Horst
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Justin M Rosenbohm
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Nikunja Kolluri
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Justin Hardick
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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38
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Mandal G, Das S, Padmanabhan S. Development of a Membrane-Based Method for Isolation of Genomic DNA from Human Blood. J Biomol Tech 2018; 29:46-53. [PMID: 29623006 DOI: 10.7171/jbt.18-2902-001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High quality and sufficient quantity of genomic DNA (gDNA) are the primary requisites of several molecular biologic applications, including clinical studies related to genetics, genomics, gene polymorphism, and DNA fingerprinting. Whole blood is the primary source of gDNA in most of the clinical investigations. Currently, commercial kits are primarily used to achieve these goals. However, the use of kits is limited by the cost and involvement of several centrifugal steps. Other methods reported are either laborious or do not produce high quality or quantity of gDNA or both. Here, we present the data on the development of a centrifugation-free, cost-effective, and user-friendly method for the isolation of human gDNA from the buffy coat of human blood that involves limited numbers of steps with about 15 min of hands-on time per sample.
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Affiliation(s)
- Goutam Mandal
- Cancyte Technologies Pvt. Ltd., Sri Shankara Research Center, Rangadore Memorial Hospital, Bangalore 560004, India
| | - Subhasish Das
- Cancyte Technologies Pvt. Ltd., Sri Shankara Research Center, Rangadore Memorial Hospital, Bangalore 560004, India
| | - Sriram Padmanabhan
- Cancyte Technologies Pvt. Ltd., Sri Shankara Research Center, Rangadore Memorial Hospital, Bangalore 560004, India
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Mauk MG, Song J, Liu C, Bau HH. Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests. BIOSENSORS 2018; 8:E17. [PMID: 29495424 PMCID: PMC5872065 DOI: 10.3390/bios8010017] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 01/10/2023]
Abstract
Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges ('chips') that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed.
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Affiliation(s)
- Michael G Mauk
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Jinzhao Song
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Changchun Liu
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Haim H Bau
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
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40
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Shah KG, Yager P. Wavelengths and Lifetimes of Paper Autofluorescence: A Simple Substrate Screening Process to Enhance the Sensitivity of Fluorescence-Based Assays in Paper. Anal Chem 2017; 89:12023-12029. [PMID: 29048155 DOI: 10.1021/acs.analchem.7b02424] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Porous media made of nitrocellulose and glass fiber are common "paper" substrates for lateral flow assays, microfluidic paper analytical devices and other point-of-care diagnostic assays. Such assays commonly use optical labels such as gold nanoparticles, latex beads, or fluorescent nanoparticles to visualize the presence of analytes. Fluorescent labels are commonly used in bioassays to enhance sensitivity, but autoluminescence of the paper substrate worsens signal-to-noise ratios of fluorescence-based assays. To date, there exists no systematic investigation of autoluminescence wavelengths or lifetimes of porous membranes used in lateral flow assays. In response, we quantified the autoluminescence of commonly used porous materials across the visible spectrum via excitation-emission spectroscopy and time-resolved fluorescence spectroscopy, and demonstrate that autoluminescence is solely due to autofluorescence with lifetimes of about 5 ns in the visible spectrum. Counterintuitively, we found that spectroscopy alone does not provide sufficient information to select candidate paper substrates for fluorophore-labeled assays. Therefore, we developed a simple quantitative framework to select a low-fluorescence substrate that minimizes both the overlap of paper and fluorophore emission spectra and the fluorescence intensity on an imaging system of interest (such as a gel imager). Use of this framework was shown to lower the limit of detection of an influenza A nucleoprotein immunoassay by over 50%. The tools developed in this manuscript enable assay developers to screen appropriate, low-fluorescence porous substrates and enhance the sensitivity of membrane-based fluorescence assays.
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Affiliation(s)
- Kamal G Shah
- Department of Bioengineering, University of Washington , Box 355061, Seattle, Washington 98195, United States
| | - Paul Yager
- Department of Bioengineering, University of Washington , Box 355061, Seattle, Washington 98195, United States
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Barreda-García S, Miranda-Castro R, de-Los-Santos-Álvarez N, Miranda-Ordieres AJ, Lobo-Castañón MJ. Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection. Anal Bioanal Chem 2017; 410:679-693. [PMID: 28932883 PMCID: PMC7079856 DOI: 10.1007/s00216-017-0620-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/18/2017] [Accepted: 09/01/2017] [Indexed: 12/22/2022]
Abstract
Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide. Currently available molecular assays, mainly based on PCR, have a limited utility in point-of-need control or resource-limited settings. Consequently, there is a strong interest in developing cost-effective, robust, and portable platforms for early detection of these harmful microorganisms. Since its description in 2004, isothermal helicase-dependent amplification (HDA) has been successfully applied in the development of novel molecular-based technologies for rapid, sensitive, and selective detection of viruses and bacteria. In this review, we highlight relevant analytical systems using this simple nucleic acid amplification methodology that takes place at a constant temperature and that is readily compatible with microfluidic technologies. Different strategies for monitoring HDA amplification products are described. In addition, we present technological advances for integrating sample preparation, HDA amplification, and detection. Future perspectives and challenges toward point-of-need use not only for clinical diagnosis but also in food safety testing and environmental monitoring are also discussed. Expanding the analytical toolbox for the detection of DNA sequences specific of pathogens with isothermal helicase dependent amplification (HDA) ![]()
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Affiliation(s)
- Susana Barreda-García
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | - Rebeca Miranda-Castro
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | | | - Arturo J Miranda-Ordieres
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | - María Jesús Lobo-Castañón
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain.
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Jiang YS, Stacy A, Whiteley M, Ellington AD, Bhadra S. Amplicon Competition Enables End-Point Quantitation of Nucleic Acids Following Isothermal Amplification. Chembiochem 2017; 18:1692-1695. [PMID: 28628741 PMCID: PMC5890436 DOI: 10.1002/cbic.201700317] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 12/22/2022]
Abstract
It is inherently difficult to quantitate nucleic acid analytes with most isothermal amplification assays. We developed loop-mediated isothermal amplification (LAMP) reactions in which competition between defined numbers of "false" and "true" amplicons leads to order of magnitude quantitation by a single endpoint determination. These thresholded LAMP reactions were successfully used to directly and quantitatively estimate the numbers of nucleic acids in complex biospecimens, including directly from cells and in sewage, with the values obtained closely correlating with qPCR quantitations. Thresholded LAMP reactions are amenable to endpoint readout by cell phone, unlike other methods that require continuous monitoring, and should therefore prove extremely useful in developing one-pot reactions for point-of-care diagnostics without needing sophisticated material or informatics infrastructure.
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Affiliation(s)
- Yu Sherry Jiang
- Department of Molecular BiosciencesCollege of Natural SciencesThe University of TexasAustinTX78712USA
- Present address: Department of ChemistryTufts University62 Talbot AvenueMedfordMA02155USA
| | - Apollo Stacy
- Department of Molecular BiosciencesCollege of Natural SciencesThe University of TexasAustinTX78712USA
| | - Marvin Whiteley
- Department of Molecular BiosciencesCollege of Natural SciencesThe University of TexasAustinTX78712USA
| | - Andrew D. Ellington
- Department of Molecular BiosciencesCollege of Natural SciencesThe University of TexasAustinTX78712USA
| | - Sanchita Bhadra
- Department of Molecular BiosciencesCollege of Natural SciencesThe University of TexasAustinTX78712USA
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New nucleic acid testing devices to diagnose infectious diseases in resource-limited settings. Eur J Clin Microbiol Infect Dis 2017; 36:1717-1731. [PMID: 28573472 DOI: 10.1007/s10096-017-3013-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/08/2017] [Indexed: 12/20/2022]
Abstract
Point-of-care diagnosis based on nucleic acid testing aims to incorporate all the analytical steps, from sample preparation to nucleic acid amplification and detection, in a single device. This device needs to provide a low-cost, robust, sensitive, specific, and easily readable analysis. Microfluidics has great potential for handling small volumes of fluids on a single platform. Microfluidic technology has recently been applied to paper, which is already used in low-cost lateral flow tests. Nucleic acid extraction from a biological specimen usually requires cell filtration and lysis on specific membranes, while affinity matrices, such as chitosan or polydiacetylene, are well suited to concentrating nucleic acids for subsequent amplification. Access to electricity is often difficult in resource-limited areas, so the amplification step needs to be equipment-free. Consequently, the reaction has to be isothermal to alleviate the need for a thermocycler. LAMP, NASBA, HDA, and RPA are examples of the technologies available. Nucleic acid detection techniques are currently based on fluorescence, colorimetry, or chemiluminescence. For point-of-care diagnostics, the results should be readable with the naked eye. Nowadays, interpretation and communication of results to health professionals could rely on a smartphone, used as a telemedicine device. The major challenge of creating an "all-in-one" diagnostic test involves the design of an optimal solution and a sequence for each analytical step, as well as combining the execution of all these steps on a single device. This review provides an overview of available materials and technologies which seem to be adapted to point-of-care nucleic acid-based diagnosis, in low-resource areas.
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Schlappi TS, McCalla SE, Schoepp NG, Ismagilov RF. Flow-through Capture and in Situ Amplification Can Enable Rapid Detection of a Few Single Molecules of Nucleic Acids from Several Milliliters of Solution. Anal Chem 2016; 88:7647-53. [PMID: 27429181 DOI: 10.1021/acs.analchem.6b01485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Detecting nucleic acids (NAs) at zeptomolar concentrations (few molecules per milliliter) currently requires expensive equipment and lengthy processing times to isolate and concentrate the NAs into a volume that is amenable to amplification processes, such as PCR or LAMP. Shortening the time required to concentrate NAs and integrating this procedure with amplification on-device would be invaluable to a number of analytical fields, including environmental monitoring and clinical diagnostics. Microfluidic point-of-care (POC) devices have been designed to address these needs, but they are not able to detect NAs present in zeptomolar concentrations in short time frames because they require slow flow rates and/or they are unable to handle milliliter-scale volumes. In this paper, we theoretically and experimentally investigate a flow-through capture membrane that solves this problem by capturing NAs with high sensitivity in a short time period, followed by direct detection via amplification. Theoretical predictions guided the choice of physical parameters for a chitosan-coated nylon membrane; these predictions can also be applied generally to other capture situations with different requirements. The membrane is also compatible with in situ amplification, which, by eliminating an elution step enables high sensitivity and will facilitate integration of this method into sample-to-answer detection devices. We tested a wide range of combinations of sample volumes and concentrations of DNA molecules using a capture membrane with a 2 mm radius. We show that for nucleic acid detection, this approach can concentrate and detect as few as ∼10 molecules of DNA with flow rates as high as 1 mL/min, handling samples as large as 50 mL. In a specific example, this method reliably concentrated and detected ∼25 molecules of DNA from 50 mL of sample.
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Affiliation(s)
- Travis S Schlappi
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Stephanie E McCalla
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Nathan G Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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Rodriguez NM, Wong WS, Liu L, Dewar R, Klapperich CM. A fully integrated paperfluidic molecular diagnostic chip for the extraction, amplification, and detection of nucleic acids from clinical samples. LAB ON A CHIP 2016; 16:753-63. [PMID: 26785636 PMCID: PMC4747825 DOI: 10.1039/c5lc01392e] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Paper diagnostics have successfully been employed to detect the presence of antigens or small molecules in clinical samples through immunoassays; however, the detection of many disease targets relies on the much higher sensitivity and specificity achieved via nucleic acid amplification tests (NAAT). The steps involved in NAAT have recently begun to be explored in paper matrices, and our group, among others, has reported on paper-based extraction, amplification, and detection of DNA and RNA targets. Here, we integrate these paper-based NAAT steps into a single paperfluidic chip in a modular, foldable system that allows for fully integrated fluidic handling from sample to result. We showcase the functionality of the chip by combining nucleic acid isolation, isothermal amplification, and lateral flow detection of human papillomavirus (HPV) 16 DNA directly from crude cervical specimens in less than 1 hour for rapid, early detection of cervical cancer. The chip is made entirely of paper and adhesive sheets, making it low-cost, portable, and disposable, and offering the potential for a point-of-care molecular diagnostic platform even in remote and resource-limited settings.
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Rodriguez NM, Linnes JC, Fan A, Ellenson CK, Pollock NR, Klapperich CM. Paper-Based RNA Extraction, in Situ Isothermal Amplification, and Lateral Flow Detection for Low-Cost, Rapid Diagnosis of Influenza A (H1N1) from Clinical Specimens. Anal Chem 2015; 87:7872-9. [PMID: 26125635 DOI: 10.1021/acs.analchem.5b01594] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The 2009 Influenza A (H1N1) pandemic disproportionately affected the developing world and highlighted the key inadequacies of traditional diagnostic methods that make them unsuitable for use in resource-limited settings, from expensive equipment and infrastructure requirements to unacceptably long turnaround times. While rapid immunoassay diagnostic tests were much less costly and more context-appropriate, they suffered from drastically low sensitivities and high false negative rates. An accurate, sensitive, and specific molecular diagnostic that is also rapid, low-cost, and independent of laboratory infrastructure is needed for effective point-of-care detection and epidemiological control in these developing regions. We developed a paper-based assay that allows for the extraction and purification of RNA directly from human clinical nasopharyngeal specimens through a poly(ether sulfone) paper matrix, H1N1-specific in situ isothermal amplification directly within the same paper matrix, and immediate visual detection on lateral flow strips. The complete sample-to-answer assay can be performed at the point-of-care in just 45 min, without the need for expensive equipment or laboratory infrastructure, and it has a clinically relevant viral load detection limit of 10(6) copies/mL, offering a 10-fold improvement over current rapid immunoassays.
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Affiliation(s)
- Natalia M Rodriguez
- †Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Jacqueline C Linnes
- †Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Andy Fan
- †Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Courtney K Ellenson
- †Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Nira R Pollock
- ‡Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Catherine M Klapperich
- †Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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