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F Silva WR, P Monteiro LC, Senra RL, D de Araújo EN, R R Cunha RO, de O Mendes TA, S Mendes JB. A biosensor based on magnetoelastic waves for detection of antibodies in human plasma for COVID-19 serodiagnosis. Biosens Bioelectron 2024; 261:116456. [PMID: 38878694 DOI: 10.1016/j.bios.2024.116456] [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: 02/15/2024] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 07/02/2024]
Abstract
This study proposes a new efficient wireless biosensor based on magnetoelastic waves for antibody detection in human plasma, aiming at the serological diagnosis of COVID-19. The biosensor underwent functionalization with the N antigen - nucleocapsid phosphoprotein of the SARS-CoV-2 virus. Validation analyses by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting (WB), atomic force microscopy (AFM), scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) microanalysis and micro-Raman spectroscopy confirmed the selectivity and effective surface functionalization of the biosensor. The research successfully obtained, expressed and purified the recombinant antigen, while plasma samples from COVID-19 positive and negative patients were applied to test the performance of the biosensor. A performance comparison with the enzyme-linked immunosorbent assays (ELISA) method revealed equivalent diagnostic capacity. These results indicate the robustness of the biosensor in reliably differentiating between positive and negative samples, highlighting its potential as an efficient and low-cost tool for the serological diagnosis of COVID-19. In addition to being fast to execute and having the potential for automation in large-scale diagnostic studies, the biosensor fills a significant gap in existing SARS-CoV-2 detection approaches.
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Affiliation(s)
- Wenderson R F Silva
- Departamento de Física, Universidade Federal de Viçosa, 36570-90, Viçosa, Minas Gerais, Brazil.
| | - Larissa C P Monteiro
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Renato Lima Senra
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Eduardo N D de Araújo
- Departamento de Física, Universidade Federal de Viçosa, 36570-90, Viçosa, Minas Gerais, Brazil
| | - Rafael O R R Cunha
- Departamento de Física, Universidade Federal de Viçosa, 36570-90, Viçosa, Minas Gerais, Brazil
| | - Tiago A de O Mendes
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Joaquim B S Mendes
- Departamento de Física, Universidade Federal de Viçosa, 36570-90, Viçosa, Minas Gerais, Brazil
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2
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Boza JM, Manning JC, Erickson DC. Comparison and Optimization of Simple DNA Extraction Methods for LAMP-Based Point-of-Care Applications Employing Submillimeter Skin Biopsies. ACS OMEGA 2024; 9:38855-38863. [PMID: 39310140 PMCID: PMC11411550 DOI: 10.1021/acsomega.4c05025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/01/2024] [Accepted: 08/13/2024] [Indexed: 09/25/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) has gained particular attention for point-of-care (POC) applications due to its advantages over traditional nucleic acid testing approaches. However, a prevailing limitation of LAMP in POC applications is nucleic acid extraction from the sample prior to analysis. This is particularly true for complex samples such as submillimeter skin biopsies where lysis and digestion involve intricate and lengthy procedures. The objective of this study was to compare alternative methodologies against the spin-column laboratory standard and evaluate them based on the World Health Organization ASSURED criteria for POC testing. Four methods-magnetic bead extraction, alkaline extraction, proteinase K-heat inactivation extraction, and boiling method extraction-were optimized utilizing porcine skin submillimeter punch biopsies and subsequently validated on human skin. Results show that both alkaline extraction and proteinase K-heat inactivation produce DNA yields equivalent to or higher than the spin-column method in porcine and human skin. When evaluated against the ASSURED criteria, both methods demonstrated low complexity while being highly scalable and readily accessible. Overall, this comparative study established a robust framework for selecting DNA extraction methods for submillimeter skin biopsies in POC applications. It also underscored the performance of the alkaline extraction method based on the ASSURED criteria, providing equivalent DNA yields to laboratory standards with reduced complexity and potential for cost-effective scalability.
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Affiliation(s)
- Juan M. Boza
- Meinig
School of Biomedical Engineering, Cornell
University, Ithaca, New York 14850, United States
| | - Jason Cade Manning
- Meinig
School of Biomedical Engineering, Cornell
University, Ithaca, New York 14850, United States
| | - David C. Erickson
- Sibley
School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14850, United States
- Division
of Nutritional Science, Cornell University, Ithaca, New York 14850, United States
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3
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Broomfield J, Kalofonou M, Bevan CL, Georgiou P. Recent Electrochemical Advancements for Liquid-Biopsy Nucleic Acid Detection for Point-of-Care Prostate Cancer Diagnostics and Prognostics. BIOSENSORS 2024; 14:443. [PMID: 39329818 PMCID: PMC11430765 DOI: 10.3390/bios14090443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 09/06/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024]
Abstract
Current diagnostic and prognostic tests for prostate cancer require specialised laboratories and have low specificity for prostate cancer detection. As such, recent advancements in electrochemical devices for point of care (PoC) prostate cancer detection have seen significant interest. Liquid-biopsy detection of relevant circulating and exosomal nucleic acid markers presents the potential for minimally invasive testing. In combination, electrochemical devices and circulating DNA and RNA detection present an innovative approach for novel prostate cancer diagnostics, potentially directly within the clinic. Recent research in electrochemical impedance spectroscopy, voltammetry, chronoamperometry and potentiometric sensing using field-effect transistors will be discussed. Evaluation of the PoC relevance of these techniques and their fulfilment of the WHO's REASSURED criteria for medical diagnostics is described. Further areas for exploration within electrochemical PoC testing and progression to clinical implementation for prostate cancer are assessed.
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Affiliation(s)
- Joseph Broomfield
- Centre for BioInspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
- Imperial Centre for Translational and Experimental Medicine, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Melpomeni Kalofonou
- Centre for BioInspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
| | - Charlotte L Bevan
- Imperial Centre for Translational and Experimental Medicine, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Pantelis Georgiou
- Centre for BioInspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
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4
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Lim J, Koprowski K, Stavins R, Xuan N, Hoang TH, Baek J, Kindratenko V, Khaertdinova L, Kim AY, Do M, King WP, Valera E, Bashir R. Point-of-Care Multiplex Detection of Respiratory Viruses. ACS Sens 2024; 9:4058-4068. [PMID: 39101394 DOI: 10.1021/acssensors.4c00992] [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] [Indexed: 08/06/2024]
Abstract
The COVID-19 pandemic, in addition to the co-occurrence of influenza virus and respiratory syncytial virus (RSV), has emphasized the requirement for efficient and reliable multiplex diagnostic methods for respiratory infections. While existing multiplex detection techniques are based on reverse transcription quantitative polymerase chain reaction (RT-qPCR) and extraction and purification kits, the need for complex instrumentation and elevated cost limit their scalability and availability. In this study, we have developed a point-of-care (POC) device based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) that can simultaneously detect four respiratory viruses (SARS-CoV-2, Influenza A, Influenza B, and RSV) and perform two controls in less than 30 min, while avoiding the use of the RNA extraction kit. The system includes a disposable microfluidic cartridge with mechanical components that automate sample processing, with a low-cost and portable optical reader and a smartphone app to record and analyze fluorescent images. The application as a real point-of-care platform was validated using swabs spiked with virus particles in nasal fluid. Our portable diagnostic system accurately detects viral RNA specific to respiratory pathogens, enabling deconvolution of coinfection information. The detection limits for each virus were determined using virus particles spiked in chemical lysis buffer. Our POC device has the potential to be adapted for the detection of new pathogens and a wide range of viruses by modifying the primer sequences. This work highlights an alternative approach for multiple respiratory virus diagnostics that is well-suited for healthcare systems in resource-limited settings or at home.
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Affiliation(s)
- Jongwon Lim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Katherine Koprowski
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Robert Stavins
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Nhat Xuan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Trung-Hieu Hoang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Janice Baek
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Victoria Kindratenko
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Liliana Khaertdinova
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Alicia Yeun Kim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Minh Do
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - William P King
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Chan Zuckerberg Biohub Chicago, Chicago, Illinois 60642, United States
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5
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Pennisi I, Cavuto ML, Miglietta L, Malpartida-Cardenas K, Stringer OW, Mantikas KT, Reid R, Frise R, Moser N, Randell P, Davies F, Bolt F, Barclay W, Holmes A, Georgiou P, Rodriguez-Manzano J. Rapid, Portable, and Electricity-free Sample Extraction Method for Enhanced Molecular Diagnostics in Resource-Limited Settings. Anal Chem 2024; 96:11181-11188. [PMID: 38967089 PMCID: PMC11256010 DOI: 10.1021/acs.analchem.4c00319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
The COVID-19 pandemic has highlighted the need for rapid and reliable diagnostics that are accessible in resource-limited settings. To address this pressing issue, we have developed a rapid, portable, and electricity-free method for extracting nucleic acids from respiratory swabs (i.e. nasal, nasopharyngeal and buccal swabs), successfully demonstrating its effectiveness for the detection of SARS-CoV-2 in residual clinical specimens. Unlike traditional approaches, our solution eliminates the need for micropipettes or electrical equipment, making it user-friendly and requiring little to no training. Our method builds upon the principles of magnetic bead extraction and revolves around a low-cost plastic magnetic lid, called SmartLid, in combination with a simple disposable kit containing all required reagents conveniently prealiquoted. Here, we clinically validated the SmartLid sample preparation method in comparison to the gold standard QIAamp Viral RNA Mini Kit from QIAGEN, using 406 clinical isolates, including 161 SARS-CoV-2 positives, using the SARS-CoV-2 RT-qPCR assays developed by the US Centers for Disease Control and Prevention (CDC). The SmartLid method showed an overall sensitivity of 95.03% (95% CI: 90.44-97.83%) and a specificity of 99.59% (95% CI: 97.76-99.99%), with a positive agreement of 97.79% (95% CI: 95.84-98.98%) when compared to QIAGEN's column-based extraction method. There are clear benefits to using the SmartLid sample preparation kit: it enables swift extraction of viral nucleic acids, taking less than 5 min, without sacrificing significant accuracy when compared to more expensive and time-consuming alternatives currently available on the market. Moreover, its simplicity makes it particularly well-suited for the point-of-care where rapid results and portability are crucial. By providing an efficient and accessible means of nucleic acid extraction, our approach aims to introduce a step-change in diagnostic capabilities for resource-limited settings.
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Affiliation(s)
- Ivana Pennisi
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Matthew L. Cavuto
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Luca Miglietta
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | | | - Oliver W. Stringer
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Katerina-Theresa Mantikas
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Ruth Reid
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Rebecca Frise
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Nicolas Moser
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Paul Randell
- Department
of Infectious Diseases, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London W6 8RP, U.K.
| | - Frances Davies
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
- Department
of Infectious Diseases, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London W6 8RP, U.K.
| | - Frances Bolt
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Wendy Barclay
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Alison Holmes
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
| | - Pantelis Georgiou
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London SW72BT, U.K.
| | - Jesus Rodriguez-Manzano
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW72AZ, U.K.
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6
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Sadique MA, Yadav S, Khan R, Srivastava AK. Engineered two-dimensional nanomaterials based diagnostics integrated with internet of medical things (IoMT) for COVID-19. Chem Soc Rev 2024; 53:3774-3828. [PMID: 38433614 DOI: 10.1039/d3cs00719g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
More than four years have passed since an inimitable coronavirus disease (COVID-19) pandemic hit the globe in 2019 after an uncontrolled transmission of the severe acute respiratory syndrome (SARS-CoV-2) infection. The occurrence of this highly contagious respiratory infectious disease led to chaos and mortality all over the world. The peak paradigm shift of the researchers was inclined towards the accurate and rapid detection of diseases. Since 2019, there has been a boost in the diagnostics of COVID-19 via numerous conventional diagnostic tools like RT-PCR, ELISA, etc., and advanced biosensing kits like LFIA, etc. For the same reason, the use of nanotechnology and two-dimensional nanomaterials (2DNMs) has aided in the fabrication of efficient diagnostic tools to combat COVID-19. This article discusses the engineering techniques utilized for fabricating chemically active E2DNMs that are exceptionally thin and irregular. The techniques encompass the introduction of heteroatoms, intercalation of ions, and the design of strain and defects. E2DNMs possess unique characteristics, including a substantial surface area and controllable electrical, optical, and bioactive properties. These characteristics enable the development of sophisticated diagnostic platforms for real-time biosensors with exceptional sensitivity in detecting SARS-CoV-2. Integrating the Internet of Medical Things (IoMT) with these E2DNMs-based advanced diagnostics has led to the development of portable, real-time, scalable, more accurate, and cost-effective SARS-CoV-2 diagnostic platforms. These diagnostic platforms have the potential to revolutionize SARS-CoV-2 diagnosis by making it faster, easier, and more accessible to people worldwide, thus making them ideal for resource-limited settings. These advanced IoMT diagnostic platforms may help with combating SARS-CoV-2 as well as tracking and predicting the spread of future pandemics, ultimately saving lives and mitigating their impact on global health systems.
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Affiliation(s)
- Mohd Abubakar Sadique
- CSIR - Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal 462026, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shalu Yadav
- CSIR - Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal 462026, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Raju Khan
- CSIR - Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal 462026, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Avanish K Srivastava
- CSIR - Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal 462026, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Baldeh M, Bawa FK, Bawah FU, Chamai M, Dzabeng F, Jebreel WMA, Kabuya JBB, Molemodile Dele-Olowu SK, Odoyo E, Rakotomalala Robinson D, Cunnington AJ. Lessons from the pandemic: new best practices in selecting molecular diagnostics for point-of-care testing of infectious diseases in sub-Saharan Africa. Expert Rev Mol Diagn 2024; 24:153-159. [PMID: 37908160 DOI: 10.1080/14737159.2023.2277368] [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: 08/31/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023]
Abstract
INTRODUCTION Point-of-care molecular diagnostics offer solutions to the limited diagnostic availability and accessibility in resource-limited settings. During the COVID-19 pandemic, molecular diagnostics became essential tools for accurate detection and monitoring of SARS-CoV-2. The unprecedented demand for molecular diagnostics presented challenges and catalyzed innovations which may provide lessons for the future selection of point-of-care molecular diagnostics. AREAS COVERED We searched PubMed from January 2020 to August 2023 to identify lessons learned from the COVID-19 pandemic which may impact the selection of point-of-care molecular diagnostics for future use in sub-Saharan Africa. We evaluated this in the context of REASSURED criteria (Real-time connectivity; Ease of specimen collection; Affordable; Sensitive; Specific; User-friendly; Rapid and robust; Equipment free; and Deliverable to users at the point of need) for point-of-care diagnostics for resource-limited settings. EXPERT OPINION The diagnostic challenges and successes during the COVID-19 pandemic affirmed the importance of the REASSURED criteria but demonstrated that these are not sufficient to ensure new diagnostics will be appropriate for public health emergencies. Capacity for rapid scale-up of diagnostic testing and transferability of assays, data, and technology are also important, resulting in updated REST-ASSURED criteria. Few diagnostics will meet all criteria, and trade-offs between criteria will need to be context-specific.
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Affiliation(s)
- Mamadu Baldeh
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Flavia K Bawa
- West African Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Faiza U Bawah
- Department of Computer Science, University of Ghana, Accra, Ghana
- Department of Computer Science and Informatics, University of Energy and Natural Resources, Sunyani, Ghana
| | - Martin Chamai
- West African Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Francis Dzabeng
- West African Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Computer Science, University of Ghana, Accra, Ghana
| | | | | | | | - Erick Odoyo
- Masinde Muliro University of Science & Technology, Kakamega, Kenya
| | | | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease and Centre for Paediatrics and Child Health, Imperial College, London, UK
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8
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Camargo BD, Cassaboni Stracke M, Soligo Sanchuki HB, de Oliveira VK, Ancelmo HC, Mozaner Bordin D, Klerynton Marchini F, Ribeiro Viana E, Blanes L. Low-Cost Arduino Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) for Sensitive Nucleic Acid Detection. BIOSENSORS 2024; 14:128. [PMID: 38534235 DOI: 10.3390/bios14030128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/05/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
This work presents a low-cost transcription loop-mediated isothermal amplification (RT-LAMP) instrument for nucleic acid detection, employing an Arduino Nano microcontroller. The cooling system includes customized printed circuit boards (PCBs) that serve as electrical resistors and incorporate fans. An aluminum block is designed to accommodate eight vials. The system also includes two PCB heaters-one for sample heating and the other for vial lid heating to prevent condensation. The color detection system comprises a TCS3200 color 8-sensor array coupled to one side of the aluminum heater body and a white 8-LED array coupled to the other side, controlled by two Multiplexer/Demultiplexer devices. LED light passes through the sample, reaching the color sensor and conveying color information crucial for detection. The top board is maintained at 110 ± 2 °C, while the bottom board is held at 65 ± 0.5 °C throughout the RT-LAMP assay. Validation tests successfully demonstrated the efficacy of the colorimetric RT-LAMP reactions using SARS-CoV-2 RNA amplification as a sample viability test, achieving 100% sensitivity and 97.3% specificity with 66 clinical samples. Our instrument offers a cost-effective (USD 100) solution with automated result interpretation and superior sensitivity compared to visual inspection. While the prototype was tested with SARS-CoV-2 RNA samples, its versatility extends to detecting other pathogens using alternative primers, showcasing its potential for broader applications in biosensing.
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Affiliation(s)
- Bruno Dias Camargo
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | - Mateus Cassaboni Stracke
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | | | - Hellen Cristina Ancelmo
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | - Dayanne Mozaner Bordin
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Fabricio Klerynton Marchini
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
| | - Emilson Ribeiro Viana
- Academic Department of Physics (DAFIS), Federal University of Technology-Paraná (UTFPR), Sete de Setembro 3165 Av., Curitiba 80230-901, Brazil
| | - Lucas Blanes
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
- Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba 81350-010, Brazil
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9
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Ngoc LTN, Lee YC. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. BIOSENSORS 2024; 14:97. [PMID: 38392016 PMCID: PMC10886876 DOI: 10.3390/bios14020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Ribonucleic acid (RNA) viruses are one of the major classes of pathogens that cause human diseases. The conventional method to detect RNA viruses is real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), but it has some limitations. It is expensive and time-consuming, with infrastructure and trained personnel requirements. Its high throughput requires sophisticated automation and large-scale infrastructure. Isothermal amplification methods have been explored as an alternative to address these challenges. These methods are rapid, user-friendly, low-cost, can be performed in less specialized settings, and are highly accurate for detecting RNA viruses. Microfluidic technology provides an ideal platform for performing virus diagnostic tests, including sample preparation, immunoassays, and nucleic acid-based assays. Among these techniques, nucleic acid isothermal amplification methods have been widely integrated with microfluidic platforms for RNA virus detection owing to their simplicity, sensitivity, selectivity, and short analysis time. This review summarizes some common isothermal amplification methods for RNA viruses. It also describes commercialized devices and kits that use isothermal amplification techniques for SARS-CoV-2 detection. Furthermore, the most recent applications of isothermal amplification-based microfluidic platforms for RNA virus detection are discussed in this article.
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Affiliation(s)
- Le Thi Nhu Ngoc
- Department of Nano Science and Technology Convergence, Gachon University, 1342 Seongnam-Daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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Chen G, Yang N, Xu L, Lu S, Chen Z, Wu F, Chen J, Zhang X. Base-Stacking-Driven Catalytic Hairpin Assembly: A Nucleic Acid Amplification Reaction Using Electrode Interface as a "Booster" for SARS-CoV-2 Point-of-Care Testing. Anal Chem 2023; 95:15595-15605. [PMID: 37820038 DOI: 10.1021/acs.analchem.3c02577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Electrochemical DNA (E-DNA) biosensors based on interface-mediated hybridization reactions are promising for point-of-care testing (POCT). However, the low efficiency of target recycle amplification and the steric hindrance at the electrode interface limit their sensing performance. Herein, we propose a base-stacking-driven catalytic hairpin assembly (BDCHA), a nucleic acid amplification reaction strategy, for POCT. The introduction of the base-stacking effect in this strategy increases the thermodynamic stability of the product, thereby effectively improving the recycling efficiency. Also, it enables the interface-mediated hybridization to maintain stability with even fewer bases in the reaction-binding domain, hence minimizing DNA secondary structure formation or intertwining at the electrode surface and ameliorating the steric hindrance limitation. The introduced base-stacking effect makes the electrode serve as a "booster" by integrating the advantages of homogeneous and heterogeneous reactions, giving BDCHA an increased reaction rate of about 20-fold, compared to the conventional catalytic hairpin assembly. As a proof of concept, our BDCHA was applied in constructing a portable E-DNA biosensor for the detection of a SARS-CoV-2 N gene sequence fragment. A simple 30 min one-pot incubation is required, and the results can be readily read on a smartphone, making it portable and user-friendly for POCT.
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Affiliation(s)
- Guanyu Chen
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Innovative Drug Research Institute, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
| | - Ning Yang
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Innovative Drug Research Institute, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
| | - Lilan Xu
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Innovative Drug Research Institute, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
| | - Shi Lu
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Innovative Drug Research Institute, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
| | - Zhuhua Chen
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Innovative Drug Research Institute, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
| | - Fang Wu
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Innovative Drug Research Institute, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
| | - Jinghua Chen
- Department of Pharmaceutical Analysis, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Innovative Drug Research Institute, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
| | - Xi Zhang
- Innovative Drug Research Institute, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
- Department of Clinical Pharmacy and Pharmacy Administration, The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province 350122, P. R. China
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11
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Messina MS, Chang CJ. Chemical Sensors and Imaging: Molecular, Materials, and Biological Platforms. ACS CENTRAL SCIENCE 2023; 9:1706-1711. [PMID: 37780366 PMCID: PMC10540294 DOI: 10.1021/acscentsci.3c01070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
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12
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Miglietta L, Chen Y, Luo Z, Xu K, Ding N, Peng T, Moniri A, Kreitmann L, Cacho-Soblechero M, Holmes A, Georgiou P, Rodriguez-Manzano J. Smart-Plexer: a breakthrough workflow for hybrid development of multiplex PCR assays. Commun Biol 2023; 6:922. [PMID: 37689821 PMCID: PMC10492832 DOI: 10.1038/s42003-023-05235-w] [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: 04/04/2023] [Accepted: 08/10/2023] [Indexed: 09/11/2023] Open
Abstract
Developing multiplex PCR assays requires extensive experimental testing, the number of which exponentially increases by the number of multiplexed targets. Dedicated efforts must be devoted to the design of optimal multiplex assays ensuring specific and sensitive identification of multiple analytes in a single well reaction. Inspired by data-driven approaches, we reinvent the process of developing and designing multiplex assays using a hybrid, simple workflow, named Smart-Plexer, which couples empirical testing of singleplex assays and computer simulation to develop optimised multiplex combinations. The Smart-Plexer analyses kinetic inter-target distances between amplification curves to generate optimal multiplex PCR primer sets for accurate multi-pathogen identification. In this study, the Smart-Plexer method is applied and evaluated for seven respiratory infection target detection using an optimised multiplexed PCR assay. Single-channel multiplex assays, together with the recently published data-driven methodology, Amplification Curve Analysis (ACA), were demonstrated to be capable of classifying the presence of desired targets in a single test for seven common respiratory infection pathogens.
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Affiliation(s)
- Luca Miglietta
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Yuwen Chen
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Zhi Luo
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Ke Xu
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Ning Ding
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Tianyi Peng
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Ahmad Moniri
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Louis Kreitmann
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Miguel Cacho-Soblechero
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, UK
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Zayed BA, Ali AN, Elgebaly AA, Talaia NM, Hamed M, Mansour FR. Smartphone-based point-of-care testing of the SARS-CoV-2: A systematic review. SCIENTIFIC AFRICAN 2023; 21:e01757. [PMID: 37351482 PMCID: PMC10256629 DOI: 10.1016/j.sciaf.2023.e01757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/03/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus's worldwide pandemic has highlighted the urgent need for reliable, quick, and affordable diagnostic tests for comprehending and controlling the epidemic by tracking the world population. Given how crucial it is to monitor and manage the pandemic, researchers have recently concentrated on creating quick detection techniques. Although PCR is still the preferred clinical diagnostic test, there is a pressing need for substitutes that are sufficiently rapid and cost-effective to provide a diagnosis at the time of use. The creation of a quick and simple POC equipment is necessary for home testing. Our review's goal is to provide an overview of the many methods utilized to identify SARS-CoV 2 in various samples utilizing portable devices, as well as any potential applications for smartphones in epidemiological research and detection. The point of care (POC) employs a range of microfluidic biosensors based on smartphones, including molecular sensors, immunological biosensors, hybrid biosensors, and imaging biosensors. For example, a number of tools have been created for the diagnosis of COVID-19, based on various theories. Integrated portable devices can be created using loop-mediated isothermal amplification, which combines isothermal amplification methods with colorimetric detection. Electrochemical approaches have been regarded as a potential substitute for optical sensing techniques that utilize fluorescence for detection and as being more beneficial to the Minimizing and simplicity of the tools used for detection, together with techniques that can amplify DNA or RNA under constant temperature conditions, without the need for repeated heating and cooling cycles. Many research have used smartphones for virus detection and data visualization, making these techniques more user-friendly and broadly distributed throughout nations. Overall, our research provides a review of different novel, non-invasive, affordable, and efficient methods for identifying COVID-19 contagious infected people and halting the disease's transmission.
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Affiliation(s)
- Berlanty A Zayed
- Tanta Student Research Academy, Faculty of Medicine, Tanta University, Tanta 31111, Egypt
| | - Ahmed N Ali
- Tanta Student Research Academy, Faculty of Medicine, Tanta University, Tanta 31111, Egypt
| | - Alaa A Elgebaly
- Tanta Student Research Academy, Faculty of Medicine, Tanta University, Tanta 31111, Egypt
| | - Nourhan M Talaia
- Tanta Student Research Academy, Faculty of Medicine, Tanta University, Tanta 31111, Egypt
| | - Mahmoud Hamed
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Tanta University, Elgeish Street, The Medical Campus of Tanta University, Tanta 31111, Egypt
| | - Fotouh R Mansour
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Tanta University, Elgeish Street, The Medical Campus of Tanta University, Tanta 31111, Egypt
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Palanisamy S, Lee LY, Kao CF, Chen WL, Wang HC, Shen ST, Jian JW, Yuan SSF, Kung YA, Wang YM. One-step-one-pot hydrothermally derived metal-organic-framework-nanohybrids for integrated point-of-care diagnostics of SARS-CoV-2 viral antigen/pseudovirus utilizing electrochemical biosensor chip. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 390:133960. [PMID: 37193120 PMCID: PMC10170875 DOI: 10.1016/j.snb.2023.133960] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic has become a global catastrophe, affecting the health and economy of the human community. It is required to mitigate the impact of pandemics by developing rapid molecular diagnostics for SARS-CoV-2 virus detection. In this context, developing a rapid point-of-care (POC) diagnostic test is a holistic approach to the prevention of COVID-19. In this context, this study aims at presenting a real-time, biosensor chip for improved molecular diagnostics including recombinant SARS-CoV-2 spike glycoprotein and SARS-CoV-2 pseudovirus detection based on one-step-one-pot hydrothermally derived CoFeBDCNH2-CoFe2O4 MOF-nanohybrids. This study was tested on a PalmSens-EmStat Go POC device, showing a limit of detection (LOD) for recombinant SARS-CoV-2 spike glycoprotein of 6.68 fg/mL and 6.20 fg/mL in buffer and 10% serum-containing media, respectively. To validate virus detection in the POC platform, an electrochemical instrument (CHI6116E) was used to perform dose dependent studies under similar experimental conditions to the handheld device. The results obtained from these studies were comparable indicating the capability and high detection electrochemical performance of MOF nanocomposite derived from one-step-one-pot hydrothermal synthesis for SARS-CoV-2 detection for the first time. Further, the performance of the sensor was tested in the presence of Omicron BA.2 and wild-type D614G pseudoviruses.
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Affiliation(s)
- Sathyadevi Palanisamy
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Li-Yun Lee
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, 75 Bo-Ai Street, Hsinchu 300, Taiwan
| | - Chih-Fei Kao
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, 75 Bo-Ai Street, Hsinchu 300, Taiwan
| | - Wen-Liang Chen
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, 75 Bo-Ai Street, Hsinchu 300, Taiwan
| | - Hsiang-Ching Wang
- Biomedical Technology and Device Research Lab, Industrial Technology Research Institute, Hsinchu 300, Taiwan
| | - San-Tai Shen
- AnTaimmu BioMed Co., Ltd, Unit 304, No. 1, Lixing 1st Road, East District, Hsinchu 300, Taiwan
| | - Jhih-Wei Jian
- AnTaimmu BioMed Co., Ltd, Unit 304, No. 1, Lixing 1st Road, East District, Hsinchu 300, Taiwan
| | - Shyng-Shiou F Yuan
- Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Faculty and College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yu-An Kung
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan City, Taiwan
| | - Yun-Ming Wang
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, 75 Bo-Ai Street, Hsinchu 300, Taiwan
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15
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Hoffmann EDR, Balzan LDR, Inamine E, Pancotto LR, Gaboardi G, Cantarelli VV. Performance of Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Targeting the RNA Polymerase Gene for the Direct Detection of SARS-CoV2 in Nasopharyngeal Swabs. Int J Mol Sci 2023; 24:13056. [PMID: 37685863 PMCID: PMC10487735 DOI: 10.3390/ijms241713056] [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: 06/11/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 09/10/2023] Open
Abstract
In 2020, a global pandemic caused by SARS-CoV-2 was declared. Different institutes proposed diagnostic molecular methods to detect the virus in clinical samples. This study aims to validate and standardize the use of a loop-mediated isothermal amplification (LAMP)-based methodology targeting the viral RP gene, as a faster and low-cost diagnostic method for SARS-CoV-2 infections. The results obtained with RT-LAMP (Reverse Transcriptase) were compared to the results of real-time polymerase chain reaction (RT-PCR) to assess its sensitivity and specificity. In total, 115 samples (nasopharyngeal samples) were used for detecting SARS-CoV-2 by RT-LAMP, with 43 positives and 72 negatives. The study showed a positive predictive value (PPV) of 90.7% and a negative predictive value (VPN) of 100%. The LAMP assay also demonstrated a high sensitivity of 90.7% and a specificity of 100% (confidence interval 77.9-97.4%) when using the lower detection limit of 40 copies/µL. The RT-LAMP described here has the potential to detect even the new variants of SARS-CoV-2, suggesting that it may not be significantly affected by gene mutations. The RT-LAMP targeting the RP viral region is faster and less expensive than other molecular approaches, making it an alternative for developing countries.
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Affiliation(s)
- Elias da Rosa Hoffmann
- Basic Health Sciences Department, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, Brazil;
- Bom Pastor Laboratory, Molecular Biology Department, Igrejinha 95650-000, Brazil
| | | | - Everton Inamine
- Central Laboratory, Santa Casa de Misericórdia de Porto Alegre, Porto Alegre 90020-090, Brazil; (E.I.)
| | - Lisiane Rech Pancotto
- Central Laboratory, Santa Casa de Misericórdia de Porto Alegre, Porto Alegre 90020-090, Brazil; (E.I.)
| | - Guilherme Gaboardi
- Biomedical Sciences Department, Serra Gaúcha University Center (FSG), Caxias do Sul 95020-472, Brazil
| | - Vlademir Vicente Cantarelli
- Basic Health Sciences Department, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, Brazil;
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Malpartida-Cardenas K, Baum J, Cunnington A, Georgiou P, Rodriguez-Manzano J. A dual paper-based nucleic acid extraction method from blood in under ten minutes for point-of-care diagnostics. Analyst 2023; 148:3036-3044. [PMID: 37265396 PMCID: PMC10291277 DOI: 10.1039/d3an00296a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023]
Abstract
Nucleic acid extraction (NAE) plays a crucial role for diagnostic testing procedures. For decades, dried blood spots (DBS) have been used for serology, drug monitoring, and molecular studies. However, extracting nucleic acids from DBS remains a significant challenge, especially when attempting to implement these applications to the point-of-care (POC). To address this issue, we have developed a paper-based NAE method using cellulose filter papers (DBSFP) that operates without the need for electricity (at room temperature). Our method allows for NAE in less than 7 min, and it involves grade 3 filter paper pre-treated with 8% (v/v) igepal surfactant, 1 min washing step with 1× PBS, and 5 min incubation at room temperature in 1× TE buffer. The performance of the methodology was assessed with loop-mediated isothermal amplification (LAMP), targeting the human reference gene beta-actin and the kelch 13 gene from P. falciparum. The developed method was evaluated against FTA cards and magnetic bead-based purification, using time-to-positive (min) for comparative analysis. Furthermore, we optimised our approach to take advantage of the dual functionality of the paper-based extraction, allowing for elution (eluted disk) as well as direct placement of the disk in the LAMP reaction (in situ disk). This flexibility extends to eukaryotic cells, bacterial cells, and viral particles. We successfully validated the method for RNA/DNA detection and demonstrated its compatibility with whole blood stored in anticoagulants. Additionally, we studied the compatibility of DBSFP with colorimetric and lateral flow detection, showcasing its potential for POC applications. Across various tested matrices, targets, and experimental conditions, our results were comparable to those obtained using gold standard methods, highlighting the versatility of our methodology. In summary, this manuscript presents a cost-effective solution for NAE from DBS, enabling molecular testing in virtually any POC setting. When combined with LAMP, our approach provides sample-to-result detection in under 35 minutes.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK.
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
| | - Jake Baum
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, UK
- School of Medical Sciences, University of New South Wales, Australia
| | - Aubrey Cunnington
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK.
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
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Ding R, Liu L, Zhang J, Lv P, Zhou L, Zhang T, Li S, Zhao R, Yang Z, Xiong P, Chen H, Wang W, Wang H, Tian Z, Liu B, Chen C. Accurate quantification of DNA using on-site PCR (osPCR) by characterizing DNA amplification at single-molecule resolution. Nucleic Acids Res 2023; 51:e65. [PMID: 37194709 PMCID: PMC10287937 DOI: 10.1093/nar/gkad388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/04/2023] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
Despite the need in various applications, accurate quantification of nucleic acids still remains a challenge. The widely-used qPCR has reduced accuracy at ultralow template concentration and is susceptible to nonspecific amplifications. The more recently developed dPCR is costly and cannot handle high-concentration samples. We combine the strengths of qPCR and dPCR by performing PCR in silicon-based microfluidic chips and demonstrate high quantification accuracy in a large concentration range. Importantly, at low template concentration, we observe on-site PCR (osPCR), where only certain sites of the channel show amplification. The sites have almost identical ct values, showing osPCR is a quasi-single molecule phenomenon. Using osPCR, we can measure both the ct values and the absolute concentration of templates in the same reaction. Additionally, osPCR enables identification of each template molecule, allowing removal of nonspecific amplification during quantification and greatly improving quantification accuracy. We develop sectioning algorithm that improves the signal amplitude and demonstrate improved detection of COVID in patient samples.
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Affiliation(s)
- Ruihua Ding
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
| | - Liying Liu
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
| | - Jiali Zhang
- School of Microelectronics, Shanghai University, Shanghai201800, China
| | - Pengxiao Lv
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
| | - Lin Zhou
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
| | - Tinglu Zhang
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai200335, China
| | - Ran Zhao
- Shanghai Center for Clinical Laboratory, Shanghai200126, China
| | - Zhuo Yang
- School of Microelectronics, Shanghai University, Shanghai201800, China
| | - Peng Xiong
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
| | - Hu Chen
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
| | - Wei Wang
- Shanghai International Travel Healthcare Center, Shanghai200335, China
| | - Hualiang Wang
- Shanghai Center for Clinical Laboratory, Shanghai200126, China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai200335, China
| | - Bo Liu
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
- School of Microelectronics, Shanghai University, Shanghai201800, China
| | - Chang Chen
- Shanghai Industrial μTechnology Research Institute (SITRI), Shanghai201800, China
- Shanghai Si-Gene Biotech Co., Ltd, Shanghai201800, China
- School of Microelectronics, Shanghai University, Shanghai201800, China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai200050, China
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18
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Malpartida-Cardenas K, Moser N, Ansah F, Pennisi I, Ahu Prah D, Amoah LE, Awandare G, Hafalla JCR, Cunnington A, Baum J, Rodriguez-Manzano J, Georgiou P. Sensitive Detection of Asymptomatic and Symptomatic Malaria with Seven Novel Parasite-Specific LAMP Assays and Translation for Use at Point-of-Care. Microbiol Spectr 2023; 11:e0522222. [PMID: 37158750 PMCID: PMC10269850 DOI: 10.1128/spectrum.05222-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
Human malaria is a life-threatening parasitic disease with high impact in the sub-Saharan Africa region, where 95% of global cases occurred in 2021. While most malaria diagnostic tools are focused on Plasmodium falciparum, there is a current lack of testing non-P. falciparum cases, which may be underreported and, if undiagnosed or untreated, may lead to severe consequences. In this work, seven species-specific loop-mediated isothermal amplification (LAMP) assays were designed and evaluated against TaqMan quantitative PCR (qPCR), microscopy, and enzyme-linked immunosorbent assays (ELISAs). Their clinical performance was assessed with a cohort of 164 samples of symptomatic and asymptomatic patients from Ghana. All asymptomatic samples with a parasite load above 80 genomic DNA (gDNA) copies per μL of extracted sample were detected with the Plasmodium falciparum LAMP assay, reporting 95.6% (95% confidence interval [95% CI] of 89.9 to 98.5) sensitivity and 100% (95% CI of 87.2 to 100) specificity. This assay showed higher sensitivity than microscopy and ELISA, which were 52.7% (95% CI of 39.7 to 67%) and 67.3% (95% CI of 53.3 to 79.3%), respectively. Nine samples were positive for P. malariae, indicating coinfections with P. falciparum, which represented 5.5% of the tested population. No samples were detected as positive for P. vivax, P. ovale, P. knowlesi, or P. cynomolgi by any method. Furthermore, translation to the point-of-care was demonstrated with a subcohort of 18 samples tested locally in Ghana using our handheld lab-on-chip platform, Lacewing, showing comparable results to a conventional fluorescence-based instrument. The developed molecular diagnostic test could detect asymptomatic malaria cases, including submicroscopic parasitemia, and it has the potential to be used for point-of-care applications. IMPORTANCE The spread of Plasmodium falciparum parasites with Pfhrp2/3 gene deletions presents a major threat to reliable point-of-care diagnosis with current rapid diagnostic tests (RDTs). Novel molecular diagnostics based on nucleic acid amplification are needed to address this liability. In this work, we overcome this challenge by developing sensitive tools for the detection of Plasmodium falciparum and non-P. falciparum species. Furthermore, we evaluate these tools with a cohort of symptomatic and asymptomatic malaria patients and test a subcohort locally in Ghana. The findings of this work could lead to the implementation of DNA-based diagnostics to fight against the spread of malaria and provide reliable, sensitive, and specific diagnostics at the point of care.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Nicolas Moser
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Ivana Pennisi
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Diana Ahu Prah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Linda Eva Amoah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Gordon Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Julius Clemence R. Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Aubrey Cunnington
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
- School of Biomedical Sciences, University of New South Wales Sydney, Sydney, Australia
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
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19
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Mao Y, Xu K, Miglietta L, Kreitmann L, Moser N, Georgiou P, Holmes A, Rodriguez-Manzano J. Deep Domain Adaptation Enhances Amplification Curve Analysis for Single-Channel Multiplexing in Real-Time PCR. IEEE J Biomed Health Inform 2023; 27:3093-3103. [PMID: 37028376 DOI: 10.1109/jbhi.2023.3257727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Data-driven approaches for molecular diagnostics are emerging as an alternative to perform an accurate and inexpensive multi-pathogen detection. A novel technique called Amplification Curve Analysis (ACA) has been recently developed by coupling machine learning and real-time Polymerase Chain Reaction (qPCR) to enable the simultaneous detection of multiple targets in a single reaction well. However, target classification purely relying on the amplification curve shapes faces several challenges, such as distribution discrepancies between different data sources (i.e., training vs testing). Optimisation of computational models is required to achieve higher performance of ACA classification in multiplex qPCR through the reduction of those discrepancies. Here, we proposed a novel transformer-based conditional domain adversarial network (T-CDAN) to eliminate data distribution differences between the source domain (synthetic DNA data) and the target domain (clinical isolate data). The labelled training data from the source domain and unlabelled testing data from the target domain are fed into the T-CDAN, which learns both domains' information simultaneously. After mapping the inputs into a domain-irrelevant space, T-CDAN removes the feature distribution differences and provides a clearer decision boundary for the classifier, resulting in a more accurate pathogen identification. Evaluation of 198 clinical isolates containing three types of carbapenem-resistant genes (blaNDM, blaIMP and blaOXA-48) illustrates a curve-level accuracy of 93.1% and a sample-level accuracy of 97.0% using T-CDAN, showing an accuracy improvement of 20.9% and 4.9% respectively. This research emphasises the importance of deep domain adaptation to enable high-level multiplexing in a single qPCR reaction, providing a solid approach to extend qPCR instruments' capabilities in real-world clinical applications.
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20
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Yu L, Tang Z, Sun Y, Yi H, Tang Y, Zhong Y, Dian D, Cong Y, Wang H, Xie Z, He S, Chen Z. A polyethylene glycol enhanced ligation-triggered self-priming isothermal amplification for the detection of SARS-CoV-2 D614G mutation. Talanta 2023; 262:124711. [PMID: 37244245 DOI: 10.1016/j.talanta.2023.124711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
We presented a polyethylene glycol (PEG) enhanced ligation-triggered self-priming isothermal amplification (PEG-LSPA) for the detection D614G mutation in S-glycoprotein of SARS-CoV-2. PEG was employed to improve the ligation efficiency of this assay by constructing a molecular crowding environment. Two hairpin probes (H1 and H2) were designed to contain 18 nt and 20 nt target binding site at their 3' end and 5' end, respectively. In presence of target sequence, it complemented with H1 and H2 to trigger ligation by ligase under molecular crowding condition to form ligated H1-H2 duplex. Then 3' terminus of the H2 would be extended by DNA polymerase under isothermal conditions to form a longer extended hairpin (EHP1). 5' terminus of EHP1 with phosphorothioate (PS) modification could form hairpin structure due to the lower Tm value. The resulting 3' end overhang would also fold back as a new primer to initiate the next round of polymerization, resulting in the formation of a longer extended hairpin (EHP2) containing two target sequence domains. In the circle of LSPA, long extended hairpin (EHPx) containing numerous target sequence domains was produced. The resulting DNA products can be monitored in real-time fluorescence signaling. Our proposed assay owns an excellent linear range from 10 fM to 10 nM with a detection limit down to 4 fM. Thus, this work provides a potential isothermal amplification method for monitoring mutations in SARS-CoV-2 variants.
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Affiliation(s)
- Luxin Yu
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Zibin Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yuanzhong Sun
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Hai Yi
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yuebiao Tang
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Yangqing Zhong
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Dongchun Dian
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Yanguang Cong
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China
| | - Houqi Wang
- School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Zhaoyang Xie
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Suhui He
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
| | - Zhangquan Chen
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China; School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China.
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21
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Tripathi P, Gulli C, Broomfield J, Alexandrou G, Kalofonou M, Bevan C, Moser N, Georgiou P. Classification of nucleic acid amplification on ISFET arrays using spectrogram-based neural networks. Comput Biol Med 2023; 161:107027. [PMID: 37211003 DOI: 10.1016/j.compbiomed.2023.107027] [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: 10/20/2022] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023]
Abstract
The COVID-19 pandemic has highlighted a significant research gap in the field of molecular diagnostics. This has brought forth the need for AI-based edge solutions that can provide quick diagnostic results whilst maintaining data privacy, security and high standards of sensitivity and specificity. This paper presents a novel proof-of-concept method to detect nucleic acid amplification using ISFET sensors and deep learning. This enables the detection of DNA and RNA on a low-cost and portable lab-on-chip platform for identifying infectious diseases and cancer biomarkers. We show that by using spectrograms to transform the signal to the time-frequency domain, image processing techniques can be applied to achieve the reliable classification of the detected chemical signals. Transformation to spectrograms is beneficial as it makes the data compatible with 2D convolutional neural networks and helps gain significant performance improvement over neural networks trained on the time domain data. The trained network achieves an accuracy of 84% with a size of 30kB making it suitable for deployment on edge devices. This facilitates a new wave of intelligent lab-on-chip platforms that combine microfluidics, CMOS-based chemical sensing arrays and AI-based edge solutions for more intelligent and rapid molecular diagnostics.
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Affiliation(s)
- Prateek Tripathi
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, SW7 2AZ, London, UK.
| | - Costanza Gulli
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, SW7 2AZ, London, UK
| | - Joseph Broomfield
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, SW7 2AZ, London, UK; Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ, London, UK
| | - George Alexandrou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, SW7 2AZ, London, UK
| | - Melpomeni Kalofonou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, SW7 2AZ, London, UK
| | - Charlotte Bevan
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ, London, UK
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, SW7 2AZ, London, UK
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, SW7 2AZ, London, UK
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22
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Biswas GC, Khan MTM, Das J. Wearable nucleic acid testing platform - A perspective on rapid self-diagnosis and surveillance of infectious diseases. Biosens Bioelectron 2023; 226:115115. [PMID: 36746023 DOI: 10.1016/j.bios.2023.115115] [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: 11/10/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Wearable biosensors (WB) are currently attracting considerable interest for rapid detection and monitoring of biomarkers including metabolites, protein, and pathogen in bodily fluids (e.g., sweat, saliva, tears, and interstitial fluid). Another branch of WB termed wearable nucleic acid testing (NAT) is blossoming thanks to the development of microfluidic technology and isothermal nucleic acid amplification technique (iNAAT); however, there are only few reports on this. The wearable NAT is an emerging field of point-of-care (POC) diagnostics, and holds the promise for time-saving self-diagnosis, and evidence-based surveillance of infectious diseases in remote or low-resource settings. The use of wearable NAT can also be advanced to include molecular diagnosis, the identification of cancer biomarkers, genetic abnormalities, and other aspects. The wearable NAT provides the potential for evidence-based surveillance of infectious diseases when combined with internet connectivity and App software. To make the wearable NAT accessible to the end users, however, improvements must be made to the fabrication, cost, speed, sensitivity, specificity, sampling, iNAAT, analyzer, and a few other features. So, in this paper, we looked at the wearable NAT's most recent development, identified its difficulties, and defined its potential for managing infectious diseases quickly in the future. This is the wearable NAT review's first effort. We expect that this article will provide the concise resources needed to develop and deploy an efficient wearable NAT system.
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Affiliation(s)
- Gokul Chandra Biswas
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
| | - Md Taufiqur Mannan Khan
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Jagotamoy Das
- Department of Chemistry, Northwestern University, 2170 Campus Dr, Evanston, IL, 60208, USA.
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23
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Naghdi T, Ardalan S, Asghari Adib Z, Sharifi AR, Golmohammadi H. Moving toward smart biomedical sensing. Biosens Bioelectron 2023; 223:115009. [PMID: 36565545 DOI: 10.1016/j.bios.2022.115009] [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: 07/02/2022] [Revised: 11/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
The development of novel biomedical sensors as highly promising devices/tools in early diagnosis and therapy monitoring of many diseases and disorders has recently witnessed unprecedented growth; more and faster than ever. Nonetheless, on the eve of Industry 5.0 and by learning from defects of current sensors in smart diagnostics of pandemics, there is still a long way to go to achieve the ideal biomedical sensors capable of meeting the growing needs and expectations for smart biomedical/diagnostic sensing through eHealth systems. Herein, an overview is provided to highlight the importance and necessity of an inevitable transition in the era of digital health/Healthcare 4.0 towards smart biomedical/diagnostic sensing and how to approach it via new digital technologies including Internet of Things (IoT), artificial intelligence, IoT gateways (smartphones, readers), etc. This review will bring together the different types of smartphone/reader-based biomedical sensors, which have been employing for a wide variety of optical/electrical/electrochemical biosensing applications and paving the way for future eHealth diagnostic devices by moving towards smart biomedical sensing. Here, alongside highlighting the characteristics/criteria that should be met by the developed sensors towards smart biomedical sensing, the challenging issues ahead are delineated along with a comprehensive outlook on this extremely necessary field.
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Affiliation(s)
- Tina Naghdi
- Nanosensors Bioplatforms Laboratory, Chemistry and Chemical Engineering Research Center of Iran, 14335-186, Tehran, Iran
| | - Sina Ardalan
- Nanosensors Bioplatforms Laboratory, Chemistry and Chemical Engineering Research Center of Iran, 14335-186, Tehran, Iran
| | - Zeinab Asghari Adib
- Nanosensors Bioplatforms Laboratory, Chemistry and Chemical Engineering Research Center of Iran, 14335-186, Tehran, Iran
| | - Amir Reza Sharifi
- Nanosensors Bioplatforms Laboratory, Chemistry and Chemical Engineering Research Center of Iran, 14335-186, Tehran, Iran
| | - Hamed Golmohammadi
- Nanosensors Bioplatforms Laboratory, Chemistry and Chemical Engineering Research Center of Iran, 14335-186, Tehran, Iran.
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24
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Deng F, Pan J, Liu Z, Zeng L, Chen J. Programmable DNA biocomputing circuits for rapid and intelligent screening of SARS-CoV-2 variants. Biosens Bioelectron 2023; 223:115025. [PMID: 36542937 PMCID: PMC9759469 DOI: 10.1016/j.bios.2022.115025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
The frequent emergence of SARS-CoV-2 variants increased viral transmissibility and reduced protection afforded by vaccines. The rapid, multichannel, and intelligent screening of variants is critical to minimizing community transmissions. DNA molecular logic gates have attracted wide attention in recent years due to the powerful information processing capabilities and molecular data biocomputing functions. In this work, some molecular switches (MSs) were connected with each other to implement arbitrary binary functions by emulating the threshold switching of MOS transistors and the decision tree model. Using specific sequences of different SARS-CoV-2 variants as inputs, the MSs net was used to build several molecular biocomputing circuits, including NOT, AND, OR, INHIBIT, XOR, half adder, half subtractor, full adder, and full subtractor. Four fluorophores (FAM, Cy3, ROX, and Cy5) were employed in the logic systems to realize the multichannel monitoring of the logic operation results. The logic response is fast and can be finished with 10 min, which facilitates the rapid wide-population screening for SARS-CoV-2 variants. Importantly, the logic results can be directly observed by the naked eye under a portable UV lamp, thus providing a simple and intelligent method to enable high-frequency point-of-care diagnostics, particularly in low-resource communities.
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Affiliation(s)
- Fang Deng
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jiafeng Pan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Lingwen Zeng
- Guangdong Langyuan Biotechnology Co., LTD, Foshan, 528313, China; School of Food Science and Engineering, Foshan University, Foshan, 528231, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.
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25
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Tarim EA, Oksuz C, Karakuzu B, Appak O, Sayiner AA, Tekin HC. Electromechanical RT-LAMP device for portable SARS-CoV-2 detection. Talanta 2023; 254:124190. [PMID: 36521325 PMCID: PMC9733968 DOI: 10.1016/j.talanta.2022.124190] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Rapid point-of-care tests for infectious diseases are essential, especially in pandemic conditions. We have developed a point-of-care electromechanical device to detect SARS-CoV-2 viral RNA using the reverse-transcription loop-mediated isothermal amplification (RT-LAMP) principle. The developed device can detect SARS-CoV-2 viral RNA down to 103 copies/mL and from a low amount of sample volumes (2 μL) in less than an hour of standalone operation without the need for professional labor and equipment. Integrated Peltier elements in the device keep the sample at a constant temperature, and an integrated camera allows automated monitoring of LAMP reaction in a stirring sample by using colorimetric analysis of unfocused sample images in the hue/saturation/value color space. This palm-fitting, portable and low-cost device does not require a fully focused sample image for analysis, and the operation could be stopped automatically through image analysis when the positive test results are obtained. Hence, viral infections can be detected with the portable device produced without the need for long, expensive, and labor-intensive tests and equipment, which can make the viral tests disseminated at the point-of-care.
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Affiliation(s)
- E. Alperay Tarim
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
| | - Cemre Oksuz
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
| | - Betul Karakuzu
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
| | - Ozgur Appak
- Department of Medical Microbiology, Dokuz Eylul University, Faculty of Medicine, Izmir 35330, Turkey
| | - Ayca Arzu Sayiner
- Department of Medical Microbiology, Dokuz Eylul University, Faculty of Medicine, Izmir 35330, Turkey
| | - H. Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey,METU MEMS Center, Ankara 06520, Turkey,Corresponding author. Department of Bioengineering, Izmir Institute of Technology, Izmir 35430, Turkey
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26
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Weerasuriya DRK, Hiniduma K, Bhakta S, Nigro LM, Posada LF, Tan H, Suib SL, Kremer R, Rusling JF. COVID-19 Detection Using a 3D-Printed Micropipette Tip and a Smartphone. ACS Sens 2023; 8:848-857. [PMID: 36689276 PMCID: PMC9888406 DOI: 10.1021/acssensors.2c02516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/27/2022] [Indexed: 01/24/2023]
Abstract
The COVID-19 pandemic has caused over 7 million deaths worldwide and over 1 million deaths in the US as of October 15, 2022. Virus testing lags behind the level or availability necessary for pandemic events like COVID-19, especially in resource-limited settings. Here, we report a low cost, mix-and-read COVID-19 assay using a synthetic SARS-CoV-2 sensor, imaged and processed using a smartphone. The assay was optimized for saliva and employs 3D-printed micropipette tips with a layer of monoclonal anti-SARS-CoV-2 inside the tip. A polymeric sensor for SARS-CoV-2 spike (S) protein (COVRs) synthesized as a thin film on silica nanoparticles provides 3,3',5-5'-tetramethylbenzidine responsive color detection using streptavidin-poly-horseradish peroxidase (ST-poly-HRP) with 400 HRP labels per molecule. COVRs were engineered with an NHS-PEG4-biotin coating to reduce nonspecific binding and provide affinity for ST-poly-HRP labels. COVRs binds to S-proteins with binding strengths and capacities much larger than salivary proteins in 10% artificial saliva-0.01%-Triton X-100 (as virus deactivator). A limit of detection (LOD) of 200 TCID50/mL (TCID50 = tissue culture infectious dose 50%) in artificial saliva was obtained using the Color Grab smartphone app and verified using ImageJ. Viral load values obtained in 10% pooled human saliva spiked with inactivated SARS-COV-2 virus gave excellent correlation with viral loads obtained from qPCR (p = 0.0003, r = 0.99).
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Affiliation(s)
- D. Randil K. Weerasuriya
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
| | - Keshani Hiniduma
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
| | - Snehasis Bhakta
- Department of Chemistry, Cooch Behar
College, Cooch Behar, WB736101, India
| | - Lisa M. Nigro
- Microbial Analysis, Resources and Services, Center for
Open Research Resources and Equipment, University of
Connecticut, Storrs, Connecticut06269-3032, United
States
- Institute for Systems Genomics,
University of Connecticut, Storrs, Connecticut06269-3003,
United States
| | - Luisa F. Posada
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
| | - Haiyan Tan
- Innovation Partnership Building at UConn Tech Park,
University of Connecticut, Storrs, Connecticut06269,
United States
| | - Steven L. Suib
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
- Institute of Materials Science,
University of Connecticut, Storrs, Connecticut06269-3136,
United States
| | - Richard Kremer
- Department of Medicine, McGill University Health
Centre, 1001 Decarie Blvd., Montreal, QCH4A,
Canada
| | - James F. Rusling
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
- Institute of Materials Science,
University of Connecticut, Storrs, Connecticut06269-3136,
United States
- Department of Surgery and Neag Cancer Center,
Uconn Health, Farmington, Connecticut06030, United
States
- School of Chemistry, National University
of Ireland at Galway, GalwayH91 TK33, Ireland
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27
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Shiaelis N, Tometzki A, Peto L, McMahon A, Hepp C, Bickerton E, Favard C, Muriaux D, Andersson M, Oakley S, Vaughan A, Matthews PC, Stoesser N, Crook DW, Kapanidis AN, Robb NC. Virus Detection and Identification in Minutes Using Single-Particle Imaging and Deep Learning. ACS NANO 2023; 17:697-710. [PMID: 36541630 PMCID: PMC9836350 DOI: 10.1021/acsnano.2c10159] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The increasing frequency and magnitude of viral outbreaks in recent decades, epitomized by the COVID-19 pandemic, has resulted in an urgent need for rapid and sensitive diagnostic methods. Here, we present a methodology for virus detection and identification that uses a convolutional neural network to distinguish between microscopy images of fluorescently labeled intact particles of different viruses. Our assay achieves labeling, imaging, and virus identification in less than 5 min and does not require any lysis, purification, or amplification steps. The trained neural network was able to differentiate SARS-CoV-2 from negative clinical samples, as well as from other common respiratory pathogens such as influenza and seasonal human coronaviruses. We were also able to differentiate closely related strains of influenza, as well as SARS-CoV-2 variants. Additional and novel pathogens can easily be incorporated into the test through software updates, offering the potential to rapidly utilize the technology in future infectious disease outbreaks or pandemics. Single-particle imaging combined with deep learning therefore offers a promising alternative to traditional viral diagnostic and genomic sequencing methods and has the potential for significant impact.
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Affiliation(s)
- Nicolas Shiaelis
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Alexander Tometzki
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Leon Peto
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- Department
of Microbiology, Oxford University Hospitals
NHS Foundation Trust, OxfordOX3 9DU, United
Kingdom
| | - Andrew McMahon
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Christof Hepp
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Erica Bickerton
- The
Pirbright Institute, Ash Road, Pirbright, Woking, SurreyGU24 0NF, United
Kingdom
| | - Cyril Favard
- Membrane
Domains and Viral Assembly, IRIM, UMR 9004 CNRS and University of Montpellier, 1919, route de Mende, 34293Montpellier, France
| | - Delphine Muriaux
- Membrane
Domains and Viral Assembly, IRIM, UMR 9004 CNRS and University of Montpellier, 1919, route de Mende, 34293Montpellier, France
- CEMIPAI, UMS 3725 CNRS and University of Montpellier, 1919, route de Mende, 34293Montpellier, France
| | - Monique Andersson
- Department
of Microbiology, Oxford University Hospitals
NHS Foundation Trust, OxfordOX3 9DU, United
Kingdom
| | - Sarah Oakley
- Department
of Microbiology, Oxford University Hospitals
NHS Foundation Trust, OxfordOX3 9DU, United
Kingdom
| | - Ali Vaughan
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- NIHR
Oxford Biomedical Research Centre, University
of Oxford, OxfordOX3 9DU, United
Kingdom
| | - Philippa C. Matthews
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Nicole Stoesser
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- NIHR
Health Protection Research Unit in Healthcare Associated Infections
and Antimicrobial Resistance, in partnership with Public Health England, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Derrick W. Crook
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- NIHR
Oxford Biomedical Research Centre, University
of Oxford, OxfordOX3 9DU, United
Kingdom
- NIHR
Health Protection Research Unit in Healthcare Associated Infections
and Antimicrobial Resistance, in partnership with Public Health England, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Achillefs N. Kapanidis
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, OxfordOX1 3QU, United Kingdom
| | - Nicole C. Robb
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
- Warwick
Medical School, University of Warwick, CoventryCV4 7AL, United Kingdom
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28
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Li D, Sun C, Mei X, Yang L. Achieving broad availability of SARS-CoV-2 detections via smartphone-based analysis. Trends Analyt Chem 2023; 158:116878. [PMID: 36506266 PMCID: PMC9728015 DOI: 10.1016/j.trac.2022.116878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
With the development of COVID-19, widely available tests are in great demand. Naked-eye SARS-CoV-2 test kits have recently been developed as home tests, but their sensitivity and accuracy are sometimes limited. Smartphones can convert various signals into digital information, potentially improving the sensitivity and accuracy of these home tests. Herein, we summarize smartphone-based detections for SARS-CoV-2. Optical detections of non-nucleic acids using various sensors and portable imaging systems, as well as nucleic acid analyses based on LAMP, CRISP, CATCH, and biosensors are discussed. Furthermore, different electrochemical detections were compared. We show results obtained using relatively complex equipment, complicated programming procedures, or custom smartphone apps, and describe methods for obtaining information with only simple setups and free software on smartphones. Then, the combined costs of typical smartphone-based detections are evaluated. Finally, the prospect of improving smartphone-based strategies to achieve broad availability of SARS-CoV-2 detection is proposed.
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Affiliation(s)
- Dan Li
- Jinzhou Medical University, Jinzhou, China
| | - Cai Sun
- AECC Shenyang Liming Aero-Engine Co, Ltd., Shenyang, China
| | - Xifan Mei
- Jinzhou Medical University, Jinzhou, China,Corresponding author
| | - Liqun Yang
- NHC Key Laboratory of Reproductive Health and Medical Genetics (China Medical University), Liaoning Research Institute of Family Planning (The Affiliated Reproductive Hospital of China Medical University), Shenyang, China,Corresponding author
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29
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Broomfield J, Kalofonou M, Pataillot-Meakin T, Powell SM, Fernandes RC, Moser N, Bevan CL, Georgiou P. Detection of YAP1 and AR-V7 mRNA for Prostate Cancer Prognosis Using an ISFET Lab-On-Chip Platform. ACS Sens 2022; 7:3389-3398. [PMID: 36368032 PMCID: PMC9706784 DOI: 10.1021/acssensors.2c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Prostate cancer (PCa) is the second most common cause of male cancer-related death worldwide. The gold standard of treatment for advanced PCa is androgen deprivation therapy (ADT). However, eventual failure of ADT is common and leads to lethal metastatic castration-resistant PCa. As such, the detection of relevant biomarkers in the blood for drug resistance in metastatic castration-resistant PCa patients could lead to personalized treatment options. mRNA detection is often limited by the low specificity of qPCR assays which are restricted to specialized laboratories. Here, we present a novel reverse-transcription loop-mediated isothermal amplification assay and have demonstrated its capability for sensitive detection of AR-V7 and YAP1 RNA (3 × 101 RNA copies per reaction). This work presents a foundation for the detection of circulating mRNA in PCa on a non-invasive lab-on-chip device for use at the point-of-care. This technique was implemented onto a lab-on-chip platform integrating an array of chemical sensors (ion-sensitive field-effect transistors) for real-time detection of RNA. Detection of RNA presence was achieved through the translation of chemical signals into electrical readouts. Validation of this technique was conducted with rapid detection (<15 min) of extracted RNA from prostate cancer cell lines 22Rv1s and DU145s.
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Affiliation(s)
- Joseph Broomfield
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, LondonSW7 2AZ, U.K.,Imperial
Centre for Translational and Experimental Medicine, Department of
Surgery and Cancer, Imperial College London, LondonW12 0NN, U.K.
| | - Melpomeni Kalofonou
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, LondonSW7 2AZ, U.K.
| | - Thomas Pataillot-Meakin
- Imperial
Centre for Translational and Experimental Medicine, Department of
Surgery and Cancer, Imperial College London, LondonW12 0NN, U.K.,Sir
Michael Uren Hub, Department of Bioengineering, Imperial College London, LondonW12 0BZ, U.K.,Molecular
Science Research Hub, Department of Chemistry, Imperial College London, LondonW12 0BZ, U.K.
| | - Sue M. Powell
- Imperial
Centre for Translational and Experimental Medicine, Department of
Surgery and Cancer, Imperial College London, LondonW12 0NN, U.K.
| | - Rayzel C. Fernandes
- Imperial
Centre for Translational and Experimental Medicine, Department of
Surgery and Cancer, Imperial College London, LondonW12 0NN, U.K.
| | - Nicolas Moser
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, LondonSW7 2AZ, U.K.
| | - Charlotte L. Bevan
- Imperial
Centre for Translational and Experimental Medicine, Department of
Surgery and Cancer, Imperial College London, LondonW12 0NN, U.K.
| | - Pantelis Georgiou
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, LondonSW7 2AZ, U.K.,
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30
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Pennisi I, Moniri A, Miscourides N, Miglietta L, Moser N, Habgood-Coote D, Herberg JA, Levin M, Kaforou M, Rodriguez-Manzano J, Georgiou P. Discrimination of bacterial and viral infection using host-RNA signatures integrated in a lab-on-chip platform. Biosens Bioelectron 2022; 216:114633. [PMID: 36081245 DOI: 10.1016/j.bios.2022.114633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/13/2022] [Accepted: 08/09/2022] [Indexed: 11/02/2022]
Abstract
The unmet clinical need for accurate point-of-care (POC) diagnostic tests able to discriminate bacterial from viral infection demands a solution that can be used both within healthcare settings and in the field, and that can also stem the tide of antimicrobial resistance. Our approach to solve this problem combine the use of host gene signatures with our Lab-on-a-Chip (LoC) technology enabling low-cost POC expression analysis to detect Infectious Disease. Transcriptomics have been extensively investigated as a potential tool to be implemented in the diagnosis of infectious disease. On the other hand, LoC technologies using ion-sensitive field-effect transistor (ISFET), in conjunction with isothermal chemistries, are offering a promising alternative to conventional amplification instruments, owing to their portable and affordable nature. Currently, the data analysis of ISFET arrays are restricted to established methods by averaging the output of every sensor to give a single time-series. This simple approach makes unrealistic assumptions, leading to insufficient performance for applications that require accurate quantification such as Host-Transcriptomics. In order to reliably quantify transcripts on our LoC platform enabling the classification of infectious disease on-chip, we propose a novel data-driven algorithm for extracting time-to-positive values from ISFET arrays. The algorithm proposed correctly outputs a time-to-positive for all the reactions, with a high correlation to RT-qLAMP (0.85, R2 = 0.98, p < 0.01), resulting in a classification accuracy of 100% (CI, 95-100%). This work aims to bridge the gap between translating assays from microarray analysis to ISFET arrays providing benefits on tackling infectious disease and diagnostic testing in hard-to-reach areas of the world.
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Affiliation(s)
- Ivana Pennisi
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK; Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
| | - Nicholas Miscourides
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
| | - Luca Miglietta
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK; Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
| | - Dominic Habgood-Coote
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Jethro A Herberg
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Michael Levin
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | | | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, UK
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31
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The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk. Int J Mol Sci 2022; 23:ijms232214110. [PMID: 36430586 PMCID: PMC9693045 DOI: 10.3390/ijms232214110] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Since the onset of the COVID-19 pandemic, over 610 million cases have been diagnosed and it has caused over 6.5 million deaths worldwide. The crisis has forced the scientific community to develop tools for disease control and management at a pace never seen before. The control of the pandemic heavily relies in the use of fast and accurate diagnostics, that allow testing at a large scale. The gold standard diagnosis of viral infections is the RT-qPCR. Although it provides consistent and reliable results, it is hampered by its limited throughput and technical requirements. Here, we discuss the main approaches to rapid and point-of-care diagnostics based on RT-qPCR and isothermal amplification diagnostics. We describe the main COVID-19 molecular diagnostic tests approved for self-testing at home or for point-of-care testing and compare the available options. We define the influence of specimen selection and processing, the clinical validation, result readout improvement strategies, the combination with CRISPR-based detection and the diagnostic challenge posed by SARS-CoV-2 variants for different isothermal amplification techniques, with a particular focus on LAMP and recombinase polymerase amplification (RPA). Finally, we try to shed light on the effect the improvement in molecular diagnostics during the COVID-19 pandemic could have in the future of other infectious diseases.
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32
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Seok Y, Yin Q, Li R, Mauk MG, Bai H, Bau HH. Manually-Operated, Slider Cassette for Multiplexed Molecular Detection at the Point of Care. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 369:132353. [PMID: 38756788 PMCID: PMC11097106 DOI: 10.1016/j.snb.2022.132353] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Effective control of epidemics, individualized medicine, and new drugs with virologic response-dependent dose and timing require, among other things, simple, inexpensive, multiplexed molecular detection platforms suitable for point of care and home use. Herein, we describe our progress towards developing such a platform that includes sample lysis, nucleic acid isolation, concentration, purification, and amplification. Our diagnostic device comprises a sliding component that houses the nucleic acid isolation membrane and a housing containing three amplification reaction chambers with dry stored reagents, blisters with buffers and wash solutions, and absorption pads to facilitate capillarity pull and waste storage. After sample introduction, the user slides the slider within the housing from one station to another to carry out various unit operations. The slider motion induces blisters to discharge their contents, effectuating washes, and eventual elution of captured nucleic acids into reaction chambers. The slider cassette mates with a processor that incubates isothermal amplification but can also be made to operate instrumentation-free. We demonstrate our cassette's utility for the co-detection of the human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV). These three blood-borne pathogens co-infect many people worldwide with severe personal and public health consequences.
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Affiliation(s)
- Youngung Seok
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 216 Towne Building, 220 S. 33 Street, Philadelphia, PA 19104, USA
| | - Qingtian Yin
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 216 Towne Building, 220 S. 33 Street, Philadelphia, PA 19104, USA
| | - Ruijie Li
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 216 Towne Building, 220 S. 33 Street, Philadelphia, PA 19104, USA
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidian District, Beijing, 100190, China
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 216 Towne Building, 220 S. 33 Street, Philadelphia, PA 19104, USA
| | - Huiwen Bai
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 216 Towne Building, 220 S. 33 Street, Philadelphia, PA 19104, USA
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, 216 Towne Building, 220 S. 33 Street, Philadelphia, PA 19104, USA
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33
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Park JW. Principles and Applications of Loop-Mediated Isothermal Amplification to Point-of-Care Tests. BIOSENSORS 2022; 12:bios12100857. [PMID: 36290994 PMCID: PMC9599884 DOI: 10.3390/bios12100857] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 05/03/2023]
Abstract
For the identification of nucleic acids, which are important biomarkers of pathogen-mediated diseases and viruses, the gold standard for NA-based diagnostic applications is polymerase chain reaction (PCR). However, the requirements of PCR limit its application as a rapid point-of-care diagnostic technique. To address the challenges associated with regular PCR, many isothermal amplification methods have been developed to accurately detect NAs. Isothermal amplification methods enable NA amplification without changes in temperature with simple devices, as well as faster amplification times compared with regular PCR. Of the isothermal amplifications, loop-mediated isothermal amplification (LAMP) is the most studied because it amplifies NAs rapidly and specifically. This review describes the principles of LAMP, the methods used to monitor the process of LAMP, and examples of biosensors that detect the amplicons of LAMP. In addition, current trends in the application of LAMP to smartphones and self-diagnosis systems for point-of-care tests are also discussed.
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Affiliation(s)
- Jee-Woong Park
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Korea
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34
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Moser N, Yu LS, Rodriguez Manzano J, Malpartida-Cardenas K, Au A, Arkell P, Cicatiello C, Moniri A, Miglietta L, Wang WH, Wang SF, Holmes A, Chen YH, Georgiou P. Quantitative detection of dengue serotypes using a smartphone-connected handheld lab-on-chip platform. Front Bioeng Biotechnol 2022; 10:892853. [PMID: 36185458 PMCID: PMC9521504 DOI: 10.3389/fbioe.2022.892853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Dengue is one of the most prevalent infectious diseases in the world. Rapid, accurate and scalable diagnostics are key to patient management and epidemiological surveillance of the dengue virus (DENV), however current technologies do not match required clinical sensitivity and specificity or rely on large laboratory equipment. In this work, we report the translation of our smartphone-connected handheld Lab-on-Chip (LoC) platform for the quantitative detection of two dengue serotypes. At its core, the approach relies on the combination of Complementary Metal-Oxide-Semiconductor (CMOS) microchip technology to integrate an array of 78 × 56 potentiometric sensors, and a label-free reverse-transcriptase loop mediated isothermal amplification (RT-LAMP) assay. The platform communicates to a smartphone app which synchronises results in real time with a secure cloud server hosted by Amazon Web Services (AWS) for epidemiological surveillance. The assay on our LoC platform (RT-eLAMP) was shown to match performance on a gold-standard fluorescence-based real-time instrument (RT-qLAMP) with synthetic DENV-1 and DENV-2 RNA and extracted RNA from 9 DENV-2 clinical isolates, achieving quantitative detection in under 15 min. To validate the portability of the platform and the geo-tagging capabilities, we led our study in the laboratories at Imperial College London, UK, and Kaohsiung Medical Hospital, Taiwan. This approach carries high potential for application in low resource settings at the point of care (PoC).
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Affiliation(s)
- Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
- *Correspondence: Nicolas Moser,
| | - Ling-Shan Yu
- Institute of Biopharmaceutical Sciences, College of Medicine, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Jesus Rodriguez Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Anselm Au
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Paul Arkell
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Chiara Cicatiello
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Luca Miglietta
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Wen-Hung Wang
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Sheng Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Yen-Hsu Chen
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
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35
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Kaci K, Del Caño R, Luna M, Milán-Rois P, Castellanos M, Abreu M, Cantón R, Galán JC, Somoza Á, Miranda R, González de Rivera G, García-Mendiola T, Lorenzo E. Paving the way to point of care (POC) devices for SARS-CoV-2 detection. Talanta 2022; 247:123542. [PMID: 35609482 PMCID: PMC9116970 DOI: 10.1016/j.talanta.2022.123542] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 01/12/2023]
Abstract
In this work we present a powerful, affordable, and portable biosensor to develop Point of care (POC) SARS-CoV-2 virus detection. It is constructed from a fast, low cost, portable and electronically automatized potentiostat that controls the potential applied to a disposable screen-printed electrochemical platform and the current response. The potentiostat was designed to get the best signal-to-noise ratio, a very simple user interface offering the possibility to be used by any device (computer, mobile phone or tablet), to have a small and portable size, and a cheap manufacturing cost. Furthermore, the device includes as main components, a data acquisition board, a controller board and a hybridization chamber with a final size of 10 × 8 × 4 cm. The device has been tested by detecting specific SARS-CoV-2 virus sequences, reaching a detection limit of 22.1 fM. Results agree well with those obtained using a conventional potentiostat, which validate the device and pave the way to the development of POC biosensors. In this sense, the device has finally applied to directly detect the presence of the virus in nasopharyngeal samples of COVID-19 patients and results confirm its utility for the rapid detection infected samples avoiding any amplification process.
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Affiliation(s)
- Karim Kaci
- HCTLab - Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Rafael Del Caño
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049, Madrid, Spain; Departamento de Química Física y Termodinámica Aplicada e Instituto Universitario de Nanoquímica, Universidad de Córdoba, 14014, Córdoba, Spain
| | - Mónica Luna
- Instituto de Micro y Nanotecnología IMN-CNM, CSIC (CEI UAM+CSIC), Isaac Newton 8, Tres Cantos, 28760, Madrid, Spain
| | - Paula Milán-Rois
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | | | - Melanie Abreu
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Álvaro Somoza
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Rodolfo Miranda
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | | | - Tania García-Mendiola
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049, Madrid, Spain; Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Encarnación Lorenzo
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049, Madrid, Spain; IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain; Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
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Lin Q, Jia K, Gou H, He H, Wen J, Shen H, Chen K, Wu Y, Lu B, Liao M, Han Y, Zhang J. A smartphone-assisted high-throughput integrated color-sensing platform for the rapid detection of Campylobacter coli. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Torezin Mendonça G, Cassaboni Stracke M, de Oliveira Coelho B, Bruna Soligo Sanchuki H, Klassen de Oliveira V, Klerynton Marchini F, Lucíola Zanette D, Nóbrega Aoki M, Ribeiro Viana E, Blanes L. A new RT-LAMP-on-a-Chip Instrument for SARS-CoV-2 diagnostics. Microchem J 2022; 180:107600. [PMID: 35620142 PMCID: PMC9121651 DOI: 10.1016/j.microc.2022.107600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 02/08/2023]
Abstract
This work describes the development of a Point-of-Care (POC) Lab-on-a-Chip (LOC) instrument for diagnosis of SARS-CoV-2 by Reverse-Transcription Loop-mediated isothermal amplification (RT-LAMP). The hardware is based on a Raspberry Pi computer ($35), a video camera, an Arduino Nano microcontroller, a printed circuit board as a heater and a 3D printed housing. The chips were manufactured in polymethyl methacrylate (PMMA) using a CO2 laser cutting machine and sealed with a PCR optic plastic film. The chip temperature is precisely controlled by a proportional-integral-derivative (PID) algorithm. During the RT-LAMP amplifications the chip was maintained at ∼ (65.0 ± 0.1) °C for 25 minutes and 5 minutes cooling down, totaling a 30 minutes of reaction .The software interpretation occurs in less than a second. The chip design has four 25 µL chambers, two for clinical samples and two for positive and negative control-samples. The RT-LAMP master mix solution added in the chip chambers contains the pH indicator Phenol Red, that is pink (for pH ∼ 8.0) before amplification and becomes yellow (pH ∼ 6.0) if the genetic material is amplified. The RT-LAMP SARS-CoV-2 diagnostic was made by color image recognition using the OpenCV machine vision software library. The software was programmed to automatically distinguish the HSV color parameter distribution in each one of the four chip chambers. The instrument was successfully tested for SARS-CoV-2 diagnosis, in 22 clinic samples, 11 positives and 11 negatives, achieving an assertiveness of 86% when compared to the results obtained by RT-LAMP standard reactions performed in conventional PCR equipment.
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Affiliation(s)
- Geovani Torezin Mendonça
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Mateus Cassaboni Stracke
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Bruna de Oliveira Coelho
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | | | - Fabricio Klerynton Marchini
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Dalila Lucíola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Emilson Ribeiro Viana
- Research and Characterization of Nanomaterials and Nanodevices Laboratory (LPCA-NN), Physics Department, Federal University of Technology - Paraná, 7 de setembro 3165 Avenue, Curitiba, Paraná, Brazil
| | - Lucas Blanes
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Corresponding author
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Van Ngoc H, Quyen TL, Vinayaka AC, Bang DD, Wolff A. Point-of-care system for rapid real-time detection of SARS-CoV-2 virus based on commercially available Arduino platforms. Front Bioeng Biotechnol 2022; 10:917573. [PMID: 35992344 PMCID: PMC9385952 DOI: 10.3389/fbioe.2022.917573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
The COVID-19 pandemic emphasized the importance of rapid, portable, and on-site testing technologies necessary for resource-limited settings for effective testing and screening to reduce spreading of the infection. Realizing this, we developed a fluorescence-based point-of-care (fPOC) detection system with real-time reverse transcriptase loop-mediated isothermal amplification for rapid and quantitative detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The system is built based on the Arduino platform compatible with commercially available open-source hardware-software and off-the-shelf electronic components. The fPOC system comprises of three main components: 1) an instrument with integrated heaters, 2) optical detection components, and 3) an injection-molded polymeric cartridge. The system was tested and experimentally proved to be able to use for fast detection of the SARS-CoV-2 virus in real-time in less than 30 min. Preliminary results of testing the performance of the fPOC revealed that the fPOC could detect the SARS-CoV-2 virus at a limit of detection (LOD50%) at two to three copies/microliter (15.36 copies/reaction), which was comparable to reactions run on a standard commercial thermocycler. The performance of the fPOC was evaluated with 12 SARS-CoV-2 clinical throat swab samples that included seven positive and five negative samples, as confirmed by reverse transcription-polymerase chain reaction. The fPOC showed 100% agreement with the commercial thermocycler. This simple design of the fPOC system demonstrates the potential to greatly enhance the practical applicability to develop a totally integrated point-of-care system for rapid on-site screening of the SARS-CoV-2 virus in the management of the pandemic.
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Affiliation(s)
- Huynh Van Ngoc
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Than Linh Quyen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Anders Wolff
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
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Zahavi M, Rohana H, Azrad M, Shinberg B, Peretz A. Rapid SARS-CoV-2 Detection Using the Lucira™ Check It COVID-19 Test Kit. Diagnostics (Basel) 2022; 12:diagnostics12081877. [PMID: 36010227 PMCID: PMC9406928 DOI: 10.3390/diagnostics12081877] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/24/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
The need for the early identification of SARS-CoV-2 has let to a quest for reliable tests that meet the standards of polymerase chain reaction (PCR) tests, on the one hand, and are low-cost, easy-to-use, and fast, on the other hand. One such test is the Lucira™ Check It COVID-19 Test kit (“Lucira”) (Lucira Health, Inc., Emeryville, CA, USA), which utilizes real-time loop-mediated isothermal amplification technology, developed for at-home use. This study evaluated the clinical sensitivity and specificity of Lucira in identifying the virus in 190 nasopharyngeal samples collected between January and October 2021. Each sample was also subjected to RT-PCR. All negative RT-PCR results were paralleled by a negative Lucira result. Out of 90 participants who had a positive RT-PCR result, 82 (91.1%) tested positive by Lucira. Among the 72 symptomatic participants, 67 (93%) tested positive by Lucira. All samples with a positive RT-PCR result with a threshold cycle (Ct) > 36, yielded a negative Lucira result. In addition, a significant positive correlation was found between Ct and time-to-positivity with Lucira (R = 0.8612, p < 0.0001). The implementation of such a portable and affordable assay may aid in breaking the COVID-19 transmission chain.
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Affiliation(s)
- Maya Zahavi
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
- Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
| | - Hanan Rohana
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
| | - Maya Azrad
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
| | - Bracha Shinberg
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
| | - Avi Peretz
- The Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Poriya, Tiberias 1528001, Israel; (M.Z.); (H.R.); (M.A.); (B.S.)
- Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel
- Correspondence: ; Tel.: +972-4-665-2322
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Zeng J, Kuang L, Cicatiello C, Sinha A, Moser N, Boutelle M, Georgiou P. A LoC Ion Imaging Platform for Spatio-Temporal Characterisation of Ion-Selective Membranes. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2022; 16:545-556. [PMID: 35763475 DOI: 10.1109/tbcas.2022.3186742] [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
In this paper, a complete Lab-on-Chip (LoC) ion imaging platform for analysing Ion-Selective Membranes (ISM) using CMOS ISFET arrays is presented. An array of 128 × 128 ISFET pixels is employed with each pixel featuring 4 transistors to bias the ISFET to a common drain amplifier. Column-level 2-step readout circuits are designed to compensate for array offset variations in a range of up to ±1 V. The chemical signal associated with a change in ionic concentration is stored and fed back to a programmable gain instrumentation amplifier for compensation and signal amplification through a global system feedback loop. This column-parallel signal pipeline also integrates an 8-bit single slope ADC and an 8-bit R-2R DAC to quantise the processed pixel output. Designed and fabricated in the TSMC 180 nm BCD process, the System-on-Chip (SoC) operates in real time with a maximum frame rate of 1000 fps, whilst occupying a silicon area of 2.3 mm × 4.5 mm. The readout platform features a high-speed digital system to perform system-level feedback compensation with a USB 3.0 interface for data streaming. With this platform we show the first reported analysis and characterisation of ISMs using an ISFETs array through capturing real-time high-speed spatio-temporal information at a resolution of 16 μm in 1000 fps, extracting time-response and sensitivity. This work paves the way of understanding the electrochemical response of ISMs, which are widely used in various biomedical applications.
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Douaki A, Garoli D, Inam AKMS, Angeli MAC, Cantarella G, Rocchia W, Wang J, Petti L, Lugli P. Smart Approach for the Design of Highly Selective Aptamer-Based Biosensors. BIOSENSORS 2022; 12:bios12080574. [PMID: 36004970 PMCID: PMC9405846 DOI: 10.3390/bios12080574] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
Aptamers are chemically synthesized single-stranded DNA or RNA oligonucleotides widely used nowadays in sensors and nanoscale devices as highly sensitive biorecognition elements. With proper design, aptamers are able to bind to a specific target molecule with high selectivity. To date, the systematic evolution of ligands by exponential enrichment (SELEX) process is employed to isolate aptamers. Nevertheless, this method requires complex and time-consuming procedures. In silico methods comprising machine learning models have been recently proposed to reduce the time and cost of aptamer design. In this work, we present a new in silico approach allowing the generation of highly sensitive and selective RNA aptamers towards a specific target, here represented by ammonium dissolved in water. By using machine learning and bioinformatics tools, a rational design of aptamers is demonstrated. This “smart” SELEX method is experimentally proved by choosing the best five aptamer candidates obtained from the design process and applying them as functional elements in an electrochemical sensor to detect, as the target molecule, ammonium at different concentrations. We observed that the use of five different aptamers leads to a significant difference in the sensor’s response. This can be explained by considering the aptamers’ conformational change due to their interaction with the target molecule. We studied these conformational changes using a molecular dynamics simulation and suggested a possible explanation of the experimental observations. Finally, electrochemical measurements exposing the same sensors to different molecules were used to confirm the high selectivity of the designed aptamers. The proposed in silico SELEX approach can potentially reduce the cost and the time needed to identify the aptamers and potentially be applied to any target molecule.
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Affiliation(s)
- Ali Douaki
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
- Correspondence: (A.D.); (P.L.)
| | - Denis Garoli
- Istituto Italiano di Tecnologia, Via Morego, 30, 16163 Genova, Italy;
| | - A. K. M. Sarwar Inam
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
| | - Martina Aurora Costa Angeli
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
| | - Giuseppe Cantarella
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genova, Italy;
| | - Jiahai Wang
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China;
| | - Luisa Petti
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
| | - Paolo Lugli
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy; (A.K.M.S.I.); (M.A.C.A.); (G.C.); (L.P.)
- Correspondence: (A.D.); (P.L.)
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Dinnes J, Sharma P, Berhane S, van Wyk SS, Nyaaba N, Domen J, Taylor M, Cunningham J, Davenport C, Dittrich S, Emperador D, Hooft L, Leeflang MM, McInnes MD, Spijker R, Verbakel JY, Takwoingi Y, Taylor-Phillips S, Van den Bruel A, Deeks JJ. Rapid, point-of-care antigen tests for diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2022; 7:CD013705. [PMID: 35866452 PMCID: PMC9305720 DOI: 10.1002/14651858.cd013705.pub3] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Accurate rapid diagnostic tests for SARS-CoV-2 infection would be a useful tool to help manage the COVID-19 pandemic. Testing strategies that use rapid antigen tests to detect current infection have the potential to increase access to testing, speed detection of infection, and inform clinical and public health management decisions to reduce transmission. This is the second update of this review, which was first published in 2020. OBJECTIVES To assess the diagnostic accuracy of rapid, point-of-care antigen tests for diagnosis of SARS-CoV-2 infection. We consider accuracy separately in symptomatic and asymptomatic population groups. Sources of heterogeneity investigated included setting and indication for testing, assay format, sample site, viral load, age, timing of test, and study design. SEARCH METHODS We searched the COVID-19 Open Access Project living evidence database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) on 08 March 2021. We included independent evaluations from national reference laboratories, FIND and the Diagnostics Global Health website. We did not apply language restrictions. SELECTION CRITERIA We included studies of people with either suspected SARS-CoV-2 infection, known SARS-CoV-2 infection or known absence of infection, or those who were being screened for infection. We included test accuracy studies of any design that evaluated commercially produced, rapid antigen tests. We included evaluations of single applications of a test (one test result reported per person) and evaluations of serial testing (repeated antigen testing over time). Reference standards for presence or absence of infection were any laboratory-based molecular test (primarily reverse transcription polymerase chain reaction (RT-PCR)) or pre-pandemic respiratory sample. DATA COLLECTION AND ANALYSIS We used standard screening procedures with three people. Two people independently carried out quality assessment (using the QUADAS-2 tool) and extracted study results. Other study characteristics were extracted by one review author and checked by a second. We present sensitivity and specificity with 95% confidence intervals (CIs) for each test, and pooled data using the bivariate model. We investigated heterogeneity by including indicator variables in the random-effects logistic regression models. We tabulated results by test manufacturer and compliance with manufacturer instructions for use and according to symptom status. MAIN RESULTS We included 155 study cohorts (described in 166 study reports, with 24 as preprints). The main results relate to 152 evaluations of single test applications including 100,462 unique samples (16,822 with confirmed SARS-CoV-2). Studies were mainly conducted in Europe (101/152, 66%), and evaluated 49 different commercial antigen assays. Only 23 studies compared two or more brands of test. Risk of bias was high because of participant selection (40, 26%); interpretation of the index test (6, 4%); weaknesses in the reference standard for absence of infection (119, 78%); and participant flow and timing 41 (27%). Characteristics of participants (45, 30%) and index test delivery (47, 31%) differed from the way in which and in whom the test was intended to be used. Nearly all studies (91%) used a single RT-PCR result to define presence or absence of infection. The 152 studies of single test applications reported 228 evaluations of antigen tests. Estimates of sensitivity varied considerably between studies, with consistently high specificities. Average sensitivity was higher in symptomatic (73.0%, 95% CI 69.3% to 76.4%; 109 evaluations; 50,574 samples, 11,662 cases) compared to asymptomatic participants (54.7%, 95% CI 47.7% to 61.6%; 50 evaluations; 40,956 samples, 2641 cases). Average sensitivity was higher in the first week after symptom onset (80.9%, 95% CI 76.9% to 84.4%; 30 evaluations, 2408 cases) than in the second week of symptoms (53.8%, 95% CI 48.0% to 59.6%; 40 evaluations, 1119 cases). For those who were asymptomatic at the time of testing, sensitivity was higher when an epidemiological exposure to SARS-CoV-2 was suspected (64.3%, 95% CI 54.6% to 73.0%; 16 evaluations; 7677 samples, 703 cases) compared to where COVID-19 testing was reported to be widely available to anyone on presentation for testing (49.6%, 95% CI 42.1% to 57.1%; 26 evaluations; 31,904 samples, 1758 cases). Average specificity was similarly high for symptomatic (99.1%) or asymptomatic (99.7%) participants. We observed a steady decline in summary sensitivities as measures of sample viral load decreased. Sensitivity varied between brands. When tests were used according to manufacturer instructions, average sensitivities by brand ranged from 34.3% to 91.3% in symptomatic participants (20 assays with eligible data) and from 28.6% to 77.8% for asymptomatic participants (12 assays). For symptomatic participants, summary sensitivities for seven assays were 80% or more (meeting acceptable criteria set by the World Health Organization (WHO)). The WHO acceptable performance criterion of 97% specificity was met by 17 of 20 assays when tests were used according to manufacturer instructions, 12 of which demonstrated specificities above 99%. For asymptomatic participants the sensitivities of only two assays approached but did not meet WHO acceptable performance standards in one study each; specificities for asymptomatic participants were in a similar range to those observed for symptomatic people. At 5% prevalence using summary data in symptomatic people during the first week after symptom onset, the positive predictive value (PPV) of 89% means that 1 in 10 positive results will be a false positive, and around 1 in 5 cases will be missed. At 0.5% prevalence using summary data for asymptomatic people, where testing was widely available and where epidemiological exposure to COVID-19 was suspected, resulting PPVs would be 38% to 52%, meaning that between 2 in 5 and 1 in 2 positive results will be false positives, and between 1 in 2 and 1 in 3 cases will be missed. AUTHORS' CONCLUSIONS Antigen tests vary in sensitivity. In people with signs and symptoms of COVID-19, sensitivities are highest in the first week of illness when viral loads are higher. Assays that meet appropriate performance standards, such as those set by WHO, could replace laboratory-based RT-PCR when immediate decisions about patient care must be made, or where RT-PCR cannot be delivered in a timely manner. However, they are more suitable for use as triage to RT-PCR testing. The variable sensitivity of antigen tests means that people who test negative may still be infected. Many commercially available rapid antigen tests have not been evaluated in independent validation studies. Evidence for testing in asymptomatic cohorts has increased, however sensitivity is lower and there is a paucity of evidence for testing in different settings. Questions remain about the use of antigen test-based repeat testing strategies. Further research is needed to evaluate the effectiveness of screening programmes at reducing transmission of infection, whether mass screening or targeted approaches including schools, healthcare setting and traveller screening.
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Affiliation(s)
- Jacqueline Dinnes
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Pawana Sharma
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sarah Berhane
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Susanna S van Wyk
- Centre for Evidence-based Health Care, Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nicholas Nyaaba
- Infectious Disease Unit, 37 Military Hospital, Cantonments, Ghana
| | - Julie Domen
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Melissa Taylor
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Clare Davenport
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | | | | | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | - René Spijker
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Medical Library, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health, Amsterdam, Netherlands
| | - Jan Y Verbakel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Yemisi Takwoingi
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Sian Taylor-Phillips
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Ann Van den Bruel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Jonathan J Deeks
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
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A Review on Potential Electrochemical Point-of-Care Tests Targeting Pandemic Infectious Disease Detection: COVID-19 as a Reference. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10070269] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fast and accurate point-of-care testing (POCT) of infectious diseases is crucial for diminishing the pandemic miseries. To fight the pandemic coronavirus disease 2019 (COVID-19), numerous interesting electrochemical point-of-care (POC) tests have been evolved to rapidly identify the causal organism SARS-CoV-2 virus, its nucleic acid and antigens, and antibodies of the patients. Many of those electrochemical biosensors are impressive in terms of miniaturization, mass production, ease of use, and speed of test, and they could be recommended for future applications in pandemic-like circumstances. On the other hand, self-diagnosis, sensitivity, specificity, surface chemistry, electrochemical components, device configuration, portability, small analyzers, and other features of the tests can yet be improved. Therefore, this report reviews the developmental trend of electrochemical POC tests (i.e., test platforms and features) reported for the rapid diagnosis of COVID-19 and correlates any significant advancements with relevant references. POCTs incorporating microfluidic/plastic chips, paper devices, nanomaterial-aided platforms, smartphone integration, self-diagnosis, and epidemiological reporting attributes are also surfed to help with future pandemic preparedness. This review especially screens the low-cost and easily affordable setups so that management of pandemic disease becomes faster and easier. Overall, the review is a wide-ranging package for finding appropriate strategies of electrochemical POCT targeting pandemic infectious disease detection.
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Filchakova O, Dossym D, Ilyas A, Kuanysheva T, Abdizhamil A, Bukasov R. Review of COVID-19 testing and diagnostic methods. Talanta 2022; 244:123409. [PMID: 35390680 PMCID: PMC8970625 DOI: 10.1016/j.talanta.2022.123409] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/09/2023]
Abstract
More than six billion tests for COVID-19 has been already performed in the world. The testing for SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) virus and corresponding human antibodies is essential not only for diagnostics and treatment of the infection by medical institutions, but also as a pre-requisite for major semi-normal economic and social activities such as international flights, off line work and study in offices, access to malls, sport and social events. Accuracy, sensitivity, specificity, time to results and cost per test are essential parameters of those tests and even minimal improvement in any of them may have noticeable impact on life in the many countries of the world. We described, analyzed and compared methods of COVID-19 detection, while representing their parameters in 22 tables. Also, we compared test performance of some FDA approved test kits with clinical performance of some non-FDA approved methods just described in scientific literature. RT-PCR still remains a golden standard in detection of the virus, but a pressing need for alternative less expensive, more rapid, point of care methods is evident. Those methods that may eventually get developed to satisfy this need are explained, discussed, quantitatively compared. The review has a bioanalytical chemistry prospective, but it may be interesting for a broader circle of readers who are interested in understanding and improvement of COVID-19 testing, helping eventually to leave COVID-19 pandemic in the past.
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Affiliation(s)
- Olena Filchakova
- Biology Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Dina Dossym
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Aisha Ilyas
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Tamila Kuanysheva
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Altynay Abdizhamil
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Rostislav Bukasov
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan.
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45
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García-Bernalt Diego J, Fernández-Soto P, Márquez-Sánchez S, Santos Santos D, Febrer-Sendra B, Crego-Vicente B, Muñoz-Bellido JL, Belhassen-García M, Corchado Rodríguez JM, Muro A. SMART-LAMP: A Smartphone-Operated Handheld Device for Real-Time Colorimetric Point-of-Care Diagnosis of Infectious Diseases via Loop-Mediated Isothermal Amplification. BIOSENSORS 2022; 12:bios12060424. [PMID: 35735571 PMCID: PMC9221248 DOI: 10.3390/bios12060424] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 05/04/2023]
Abstract
Nucleic acid amplification diagnostics offer outstanding features of sensitivity and specificity. However, they still lack speed and robustness, require extensive infrastructure, and are neither affordable nor user-friendly. Thus, they have not been extensively applied in point-of-care diagnostics, particularly in low-resource settings. In this work, we have combined the loop-mediated isothermal amplification (LAMP) technology with a handheld portable device (SMART-LAMP) developed to perform real-time isothermal nucleic acid amplification reactions, based on simple colorimetric measurements, all of which are Bluetooth-controlled by a dedicated smartphone app. We have validated its diagnostic utility regarding different infectious diseases, including Schistosomiasis, Strongyloidiasis, and COVID-19, and analyzed clinical samples from suspected COVID-19 patients. Finally, we have proved that the combination of long-term stabilized LAMP master mixes, stored and transported at room temperature with our developed SMART-LAMP device, provides an improvement towards true point-of-care diagnosis of infectious diseases in settings with limited infrastructure. Our proposal could be easily adapted to the diagnosis of other infectious diseases.
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Affiliation(s)
- Juan García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (B.F.-S.); (B.C.-V.)
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (B.F.-S.); (B.C.-V.)
- Correspondence: (P.F.-S.); (A.M.); Tel.: +34-677596173 (ext. 6861) (P.F.-S.)
| | - Sergio Márquez-Sánchez
- BISITE Research Group, University of Salamanca, Calle Espejo s/n. Edificio Multiusos I+D+i, 37007 Salamanca, Spain; (S.M.-S.); (D.S.S.); (J.M.C.R.)
- Air Institute, IoT Digital Innovation Hub (Spain), 37188 Salamanca, Spain
| | - Daniel Santos Santos
- BISITE Research Group, University of Salamanca, Calle Espejo s/n. Edificio Multiusos I+D+i, 37007 Salamanca, Spain; (S.M.-S.); (D.S.S.); (J.M.C.R.)
| | - Begoña Febrer-Sendra
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (B.F.-S.); (B.C.-V.)
| | - Beatriz Crego-Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (B.F.-S.); (B.C.-V.)
| | - Juan Luis Muñoz-Bellido
- Microbiology and Parasitology Service, Complejo Asistencial Universitario de Salamanca, University of Salamanca, 37007 Salamanca, Spain;
| | - Moncef Belhassen-García
- Internal Medicine Service, Infectious Diseases Section, Complejo Asistencial Universitario de Salamanca, University of Salamanca, 37007 Salamanca, Spain;
| | - Juan M. Corchado Rodríguez
- BISITE Research Group, University of Salamanca, Calle Espejo s/n. Edificio Multiusos I+D+i, 37007 Salamanca, Spain; (S.M.-S.); (D.S.S.); (J.M.C.R.)
- Air Institute, IoT Digital Innovation Hub (Spain), 37188 Salamanca, Spain
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (B.F.-S.); (B.C.-V.)
- Correspondence: (P.F.-S.); (A.M.); Tel.: +34-677596173 (ext. 6861) (P.F.-S.)
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Asghar R, Rasheed M, ul Hassan J, Rafique M, Khan M, Deng Y. Advancements in Testing Strategies for COVID-19. BIOSENSORS 2022; 12:410. [PMID: 35735558 PMCID: PMC9220779 DOI: 10.3390/bios12060410] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 coronavirus, also known as the disease-causing agent for COVID-19, is a virulent pathogen that may infect people and certain animals. The global spread of COVID-19 and its emerging variation necessitates the development of rapid, reliable, simple, and low-cost diagnostic tools. Many methodologies and devices have been developed for the highly sensitive, selective, cost-effective, and rapid diagnosis of COVID-19. This review organizes the diagnosis platforms into four groups: imaging, molecular-based detection, serological testing, and biosensors. Each platform's principle, advancement, utilization, and challenges for monitoring SARS-CoV-2 are discussed in detail. In addition, an overview of the impact of variants on detection, commercially available kits, and readout signal analysis has been presented. This review will expand our understanding of developing advanced diagnostic approaches to evolve into susceptible, precise, and reproducible technologies to combat any future outbreak.
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Affiliation(s)
- Rabia Asghar
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Madiha Rasheed
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
| | - Jalees ul Hassan
- Department of Wildlife and Ecology, Faculty of Fisheries and Wildlife, University of Veterinary and Animal Sciences-UVAS, Lahore 54000, Pakistan;
| | - Mohsin Rafique
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China;
| | - Mashooq Khan
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China;
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China;
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47
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The potential of digital molecular diagnostics for infectious diseases in sub-Saharan Africa. PLOS DIGITAL HEALTH 2022; 1:e0000064. [PMID: 36812544 PMCID: PMC9931288 DOI: 10.1371/journal.pdig.0000064] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
There is a large gap between diagnostic needs and diagnostic access across much of sub-Saharan Africa (SSA), particularly for infectious diseases that inflict a substantial burden of morbidity and mortality. Accurate diagnostics are essential for the correct treatment of individuals and provide vital information underpinning disease surveillance, prevention, and control strategies. Digital molecular diagnostics combine the high sensitivity and specificity of molecular detection with point-of-care format and mobile connectivity. Recent developments in these technologies create an opportunity for a radical transformation of the diagnostic ecosystem. Rather than trying to emulate diagnostic laboratory models in resource-rich settings, African countries have the potential to pioneer new models of healthcare designed around digital diagnostics. This article describes the need for new diagnostic approaches, highlights advances in digital molecular diagnostic technology, and outlines their potential for tackling infectious diseases in SSA. It then addresses the steps that will be necessary for the development and implementation of digital molecular diagnostics. Although the focus is on infectious diseases in SSA, many of the principles apply to other resource-limited settings and to noncommunicable diseases.
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48
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Wormald BW, Moser N, deSouza NM, Mantikas KT, Malpartida-Cardenas K, Pennisi I, Ind TEJ, Vroobel K, Kalofonou M, Rodriguez-Manzano J, Georgiou P. Lab-on-chip assay of tumour markers and human papilloma virus for cervical cancer detection at the point-of-care. Sci Rep 2022; 12:8750. [PMID: 35610285 PMCID: PMC9128326 DOI: 10.1038/s41598-022-12557-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/22/2022] [Indexed: 01/17/2023] Open
Abstract
Cervical cancer affects over half a million people worldwide each year, the majority of whom are in resource-limited settings where cytology screening is not available. As persistent human papilloma virus (HPV) infections are a key causative factor, detection of HPV strains now complements cytology where screening services exist. This work demonstrates the efficacy of a handheld Lab-on-Chip (LoC) device, with an external sample extraction process, in detecting cervical cancer from biopsy samples. The device is based on Ion-Sensitive Field-Effect Transistor (ISFET) sensors used in combination with loop-mediated isothermal amplification (LAMP) assays, to amplify HPV DNA and human telomerase reverse transcriptase (hTERT) mRNA. These markers were selected because of their high levels of expression in cervical cancer cells, but low to nil expression in normal cervical tissue. The achieved analytical sensitivity for the molecular targets resolved down to a single copy per reaction for the mRNA markers, achieving a limit of detection of 102 for hTERT. In the tissue samples, HPV-16 DNA was present in 4/5 malignant and 2/5 benign tissues, with HPV-18 DNA being present in 1/5 malignant and 1/5 benign tissues. hTERT mRNA was detected in all malignant and no benign tissues, with the demonstrated pilot data to indicate the potential for using the LoC in cervical cancer screening in resource-limited settings on a large scale.
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Affiliation(s)
- Benjamin W Wormald
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, Institute of Cancer Research, London, SW7 3RP, UK
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2BT, UK
| | - Nandita M deSouza
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, Institute of Cancer Research, London, SW7 3RP, UK
| | - Katerina-Theresa Mantikas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2BT, UK
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2BT, UK
| | - Ivana Pennisi
- Department of Infectious Disease, Imperial College London, School of Medicine, St Mary's Hospital, London, W2 1NY, UK
| | - Thomas E J Ind
- Department of Surgical Oncology, Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Katherine Vroobel
- Department of Pathology, Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Melpomeni Kalofonou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2BT, UK
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Imperial College London, School of Medicine, St Mary's Hospital, London, W2 1NY, UK
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2BT, UK.
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49
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Savonnet M, Aubret M, Laurent P, Roupioz Y, Cubizolles M, Buhot A. Kinetics of Isothermal Dumbbell Exponential Amplification: Effects of Mix Composition on LAMP and Its Derivatives. BIOSENSORS 2022; 12:bios12050346. [PMID: 35624647 PMCID: PMC9138685 DOI: 10.3390/bios12050346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an exponential amplification method of DNA strands that is more and more used for its high performances. Thanks to its high sensitivity and selectivity, LAMP found numerous applications from the detection of pathogens or viruses through their genome amplification to its incorporation as an amplification strategy in protein or miRNA biomarker quantification. The LAMP method is composed of two stages: the first one consists in the transformation of the DNA strands into dumbbell structures formed of two stems and loops thanks to four primers; then, in the second stage, only two primers are required to amplify the dumbbells exponentially in numerous hairpins of increasing lengths. In this paper, we propose a theoretical framework to analyze the kinetics of the second stage of LAMP, the isothermal dumbbell exponential amplification (IDEA) as function of the physico-chemical parameters of the amplification reaction. Dedicated experiments validate the models. We believe these results may help the optimization of LAMP performances by reducing the number of experiments necessary to find the best parameters.
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Affiliation(s)
- Maud Savonnet
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Mathilde Aubret
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Patricia Laurent
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Yoann Roupioz
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
| | - Myriam Cubizolles
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
- Correspondence: (M.C.); (A.B.)
| | - Arnaud Buhot
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Correspondence: (M.C.); (A.B.)
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50
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Song W, Zhang T, Lin H, Yang Y, Zhao G, Huang X. Conventional and Microfluidic Methods for the Detection of Nucleic Acid of SARS-CoV-2. MICROMACHINES 2022; 13:636. [PMID: 35457940 PMCID: PMC9031662 DOI: 10.3390/mi13040636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 12/23/2022]
Abstract
Nucleic acid testing (NAT) played a crucial role in containing the spread of SARS-CoV-2 during the epidemic. The gold standard technique, the quantitative real-time polymerase chain reaction (qRT-PCR) technique, is currently used by the government and medical boards to detect SARS-CoV-2. Due to the limitations of this technology, it is not capable of meeting the needs of large-scale rapid detection. To solve this problem, many new techniques for detecting nucleic acids of SARS-CoV-2 have been reported. Therefore, a review that systematically and comprehensively introduces and compares various detection technologies is needed. In this paper, we not only review the traditional NAT but also provide an overview of microfluidic-based NAT technologies and summarize and discuss the characteristics and development prospects of these techniques.
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Affiliation(s)
| | | | | | | | | | - Xiaowen Huang
- State Key Laboratory of Biobased Material and Green Papermaking, Department of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250300, China; (W.S.); (T.Z.); (H.L.); (Y.Y.); (G.Z.)
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