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Fry J, Lee JYH, McAuley JL, Porter JL, Monk IR, Martin ST, Collins DJ, Barbante GJ, Fitzgerald NJ, Stinear TP. Optimization of Reverse Transcription Loop-Mediated Isothermal Amplification for In Situ Detection of SARS-CoV-2 in a Micro-Air-Filtration Device Format. ACS OMEGA 2024; 9:40832-40840. [PMID: 39372017 PMCID: PMC11447726 DOI: 10.1021/acsomega.4c05784] [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: 06/20/2024] [Revised: 09/06/2024] [Accepted: 09/11/2024] [Indexed: 10/08/2024]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic has supercharged innovation in the field of molecular diagnostics and led to the exploration of systems that permit the autonomous identification of airborne infectious agents. Airborne virus detection is an emerging approach for determining exposure risk, although current methods limit intervention timeliness. Here, we explore reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for one-pot detection of Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) (SCV2) run on membrane filters suitable for micro-air-filtration of airborne viruses. We use a design of experiments statistical framework to establish the optimal additive composition for running RT-LAMP on membrane filters. Using SCV2 liquid spike-in experiments and fluorescence detection, we show that single-pot RT-LAMP on glass fiber filters reliably detected 0.10 50% tissue culture infectious dose (TCID50) SCV2 per reaction (3600 E-gene copies) and is an order of magnitude more sensitive than conventional RT-LAMP.
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Affiliation(s)
- Jacob Fry
- ARC
Centre of Excellence in Exciton Science, The School of Chemistry, The University of Melbourne, Masson Rd, Parkville, Victoria 3010, Australia
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Jean Y. H. Lee
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Julie L. McAuley
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Jessica L. Porter
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Ian R. Monk
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Samuel T. Martin
- Department
of Biomedical Engineering, The University
of Melbourne, Building
261/203 Bouverie St, Carlton, Victoria 3053, Australia
| | - David J. Collins
- Department
of Biomedical Engineering, The University
of Melbourne, Building
261/203 Bouverie St, Carlton, Victoria 3053, Australia
- Graeme
Clarke Institute, The University of Melbourne, Chemical Engineering 2 Building
167, Parkville, Victoria 3010, Australia
| | - Gregory J. Barbante
- Defence
Science and Technology Group, Australian
Department of Defence, 506 Lorimer Street, Fishermans Bend, Victoria 3207, Australia
| | - Nicholas J. Fitzgerald
- Defence
Science and Technology Group, Australian
Department of Defence, 506 Lorimer Street, Fishermans Bend, Victoria 3207, Australia
| | - Timothy P. Stinear
- Department
of Microbiology and Immunology, The Doherty Institute for Infection
and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
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Otero J, Rodríguez-Lázaro MA, Martínez-Trejo A, Mbanze D, Solana G, Vergara A, Bosch S, Gozal D, Vila J, Farré R. Robust and low-cost open-source device for detecting infectious microorganisms by loop-mediated isothermal amplification. HARDWAREX 2024; 19:e00568. [PMID: 39291286 PMCID: PMC11405915 DOI: 10.1016/j.ohx.2024.e00568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/10/2024] [Accepted: 08/09/2024] [Indexed: 09/19/2024]
Abstract
Loop-Mediated Isothermal Amplification (LAMP) is a useful technique for detecting infectious microorganisms in human fluids since it performs similarly to conventional PCR, the results are obtained faster and no thermocyclers or complex devices are required. Since only two isothermal blocks (95 °C to lyse cells and 65 °C for DNA amplification) are needed, LAMP is particularly suited for applications in Low- and Middle-Income Countries (LMICs). To validate such assumption, we first designed and tested Arduino-controlled LAMP thermoblocks to process a considerable number of samples simultaneously with a low-energy consumption to enable routine use under worst-case conditions (no main power source and low ambient temperatures). The thermoblocks were tested when battery-powered at temperature down to 5 °C, showing high stability in well temperatures (<0.8 °C). The charge required for both thermoblocks to simultaneously achieve the target temperatures after switching on and to keep their working temperatures were 4.1 A·h and 2.4 A·h/h, respectively. Second, we implemented a low-cost viewer with LEDs and filters to detect the fluorescent LAMP reaction. All the components required for the instrument are for general purpose and readily available by e-commerce. Thus, the LAMP device allows for considerable autonomy by using a typical car battery in rural and itinerant healthcare or field hospitals in LMICs, even under difficult environmental conditions.
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Affiliation(s)
- Jorge Otero
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona. Casanova 143, 08036 Barcelona, Spain
- CIBER de Enfermedades Respiratorias. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Miguel A Rodríguez-Lázaro
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona. Casanova 143, 08036 Barcelona, Spain
| | - Arturo Martínez-Trejo
- ISGlobal, Barcelona. Roselló 132, 08028 Barcelona, Spain
- School of Medicine and Health Sciences, University of Barcelona. Casanova 143, 08036 Barcelona, Spain
| | - Daniel Mbanze
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona. Casanova 143, 08036 Barcelona, Spain
- Faculdade de Engenharias e Tecnologias, Universidade Save. Av. Américo Boavida s/n, Maxixe, Inhambane, Mozambique
| | - Gorka Solana
- Faculdade de Engenharias e Tecnologias, Universidade Save. Av. Américo Boavida s/n, Maxixe, Inhambane, Mozambique
| | - Andrea Vergara
- Hospital Clínic of Barcelona, University of Barcelona. Villaroel 170, 08036 Barcelona, Spain
- CIBER de Enfermedades Infecciosas. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Salvador Bosch
- Department of Applied Physics, School of Physics, University of Barcelona. Martí Franqués 1, 08028 Barcelona, Spain
| | - David Gozal
- Office of the Dean, Joan C. Edwards School of Medicine, Marshall University, 1600 Medical Center Dr, WV 25701, Huntington, WV, USA
| | - Jordi Vila
- ISGlobal, Barcelona. Roselló 132, 08028 Barcelona, Spain
- Hospital Clínic of Barcelona, University of Barcelona. Villaroel 170, 08036 Barcelona, Spain
- CIBER de Enfermedades Infecciosas. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Ramon Farré
- Unit of Biophysics and Bioengineering, School of Medicine and Health Sciences, University of Barcelona. Casanova 143, 08036 Barcelona, Spain
- CIBER de Enfermedades Respiratorias. Monforte de Lemos 3-5, 28029 Madrid, Spain
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Zhang J, Xu L, Sheng Z, Zheng J, Chen W, Hu Q, Shen F. Combination-Lock SlipChip Integrating Nucleic Acid Sample Preparation and Isothermal LAMP Amplification for the Detection of SARS-CoV-2. ACS Sens 2024; 9:646-653. [PMID: 38181090 DOI: 10.1021/acssensors.3c01727] [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: 01/07/2024]
Abstract
Nucleic acid analysis with an easy-to-use workflow, high specificity and sensitivity, independence of sophisticated instruments, and accessibility outside of the laboratory is highly desirable for the detection and monitoring of infectious diseases. Integration of laboratory-quality sample preparation on a hand-held system is critical for performance. A SlipChip device inspired by the combination lock can perform magnetic bead-based nucleic acid extraction with several clockwise and counterclockwise rotations. A palm-sized base station was developed to assist sample preparation and provide thermal control of isothermal nucleic acid amplification without plug-in power. The loop-mediated isothermal amplification reaction can be performed with a colorimetric method and directly analyzed by the naked eye or with a mobile phone app. This system achieves good bead recovery during the sample preparation workflow and has minimal residue carryover from the lysis and elution buffers. Its performance is comparable to that of the standard laboratory protocol with real-time qPCR amplification methods. The entire workflow is completed in less than 35 min and the device can achieve 500 copies/mL sensitivity. Thirty clinical nasal swab samples were collected and tested with a sensitivity of 95% and a specificity of 100% for SARS-CoV-2. This combination-lock SlipChip provides a promising fast, easy-to-use nucleic acid test with bead-based sample preparation that produces laboratory-quality results for point-of-care settings, especially in home use applications.
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Affiliation(s)
- Jiajie Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Lei Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Zheyi Sheng
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Jiayi Zheng
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Weiyu Chen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
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Pauly MD, Weis-Torres S, Hayden TM, Ganova-Raeva LM, Kamili S. Development of simple, rapid, and sensitive methods for detection of hepatitis C virus RNA from whole blood using reverse transcription loop-mediated isothermal amplification. J Clin Microbiol 2023; 61:e0077123. [PMID: 37933990 PMCID: PMC10662345 DOI: 10.1128/jcm.00771-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023] Open
Abstract
Hepatitis C virus (HCV) infection is an underdiagnosed global health problem. Diagnosis of current HCV infections typically requires testing for HCV RNA using high-complexity laboratory tests. Methods for the detection of HCV RNA that are simple, inexpensive, rapid, and compatible with use outside of a laboratory setting are very important in order to improve access to hepatitis C diagnostic testing and facilitate accelerated linkage to care. We developed and evaluated three simple workflows for extracting HCV RNA from small volumes of whole blood for use in a sensitive, pan-genotypic RT-LAMP assay. The water workflow uses osmotic stress to release HCV RNA and has a limit of detection of 4.3 log10(IU/mL) (95% CI 4.0-4.9). The heat workflow uses a heating step to release HCV RNA and has a limit of detection of 4.2 log10(IU/mL) (95% CI 3.8-5.1). The bead workflow, which uses chemical lysis of the sample and a streamlined paramagnetic solid phase reversible immobilization bead procedure for nucleic acid purification, has a limit of detection of 2.8 log10(IU/mL) (95% CI 2.5-3.4). When used to test whole blood spiked with HCV RNA-positive plasma samples in which most HCV levels were below 5.0 log10(IU/mL), the water, heat, and bead workflows detected HCV RNA in 69%, 75%, and 94% of samples, respectively. These workflows are compatible with visual lateral flow dipsticks, and each takes less than 60 min from sample to result. Each workflow can be performed with minimal and inexpensive equipment. With further procedural simplifications, these workflows may form the basis of assays for the point-of-care diagnosis of HCV infections.
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Affiliation(s)
- Matthew D. Pauly
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Sabrina Weis-Torres
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Tonya M. Hayden
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Lilia M. Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Saleem Kamili
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
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Blin M, Senghor B, Boissier J, Mulero S, Rey O, Portela J. Development of environmental loop-mediated isothermal amplification (eLAMP) diagnostic tool for Bulinus truncatus field detection. Parasit Vectors 2023; 16:78. [PMID: 36855192 PMCID: PMC9972309 DOI: 10.1186/s13071-023-05705-4] [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: 11/24/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Global changes are reshaping the distribution of vector-borne diseases by spreading vectors to previously non-endemic areas. Since 2013, urogenital schistosomiasis has emerged in Corsica and threatens European countries. Gastropod vectors release schistosome larvae that can infect humans who come into contact with freshwater bodies. Monitoring schistosomiasis host vectors is a prerequisite to understand and subsequently to control this pathogen transmission. Because malacological surveys are time consuming and require special expertise, the use of a simple molecular method is desirable. METHODS The aim of this study is to develop a ready-to-use protocol using the LAMP (loop-mediated isothermal amplification) method to detect environmental DNA of Bulinus truncatus, vector of Schistosoma haematobium. Interestingly, LAMP method possesses all the characteristics required for adaptability to field conditions particularly in low-income countries: speed, simplicity, lyophilized reagents, low cost and robustness against DNA amplification inhibitors. We have tested this new method on Corsican water samples previously analysed by qPCR and ddPCR. RESULTS We demonstrate that our diagnostic tool B. truncatus eLAMP (Bt-eLAMP) can detect the eDNA of Bulinus truncatus as effectively as the two other methods. Bt-eLAMP can even detect 1/4 of positive samples not detectable by qPCR. Moreover, the complete Bt-eLAMP protocol (sampling, sample pre-process, amplification and revelation) does not require sophisticated equipment and can be done in 1 ½ h. CONCLUSIONS LAMP detection of environmental DNA provides large-scale sensitive surveillance of urogenital schistosomiasis possible by identifying potentially threatened areas. More generally, eLAMP method has great potential in vector-borne diseases and ecology.
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Affiliation(s)
- Manon Blin
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan, Via Domitia, 66860, Perpignan, France. .,SAS ParaDev®, 66860, Perpignan, France.
| | - Bruno Senghor
- VITROME, IRD-UCAD International Campus, 1386 Dakar, Senegal
| | - Jérôme Boissier
- grid.11136.340000 0001 2192 5916Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan, Via Domitia, 66860 Perpignan, France
| | - Stephen Mulero
- grid.11136.340000 0001 2192 5916Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan, Via Domitia, 66860 Perpignan, France ,Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS-LECA, 38000 Grenoble, France
| | - Olivier Rey
- grid.11136.340000 0001 2192 5916Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan, Via Domitia, 66860 Perpignan, France
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McCloskey D, Boza J, Mason CE, Erickson D. MINI: A high-throughput point-of-care device for performing hundreds of nucleic acid tests per day. Biosens Bioelectron 2022; 216:114654. [PMID: 36084523 PMCID: PMC10960951 DOI: 10.1016/j.bios.2022.114654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/11/2022] [Accepted: 08/20/2022] [Indexed: 11/24/2022]
Abstract
There are a variety of infectious diseases with a high incidence and mortality in limited resource settings that could benefit from rapid point of care molecular diagnosis. Global health efforts have sought to implement mass-screening programs to provide earlier detection and subsequent treatment in an effort to control transmission and improve health outcomes. However, many of the current diagnostic technologies under development are limited to fewer than 10 samples per run, which inherently restricts the screening throughput of these devices. We have developed a high throughput device called "MINI" that is capable of testing hundreds of samples per day at the point-of-care. MINI can utilize multiple energy sources - electricity, flame, or solar - to perform loop-mediated isothermal amplification (LAMP) in a portable and robust device which is ideal for use in limited resource settings. The unique opto-electronic design of MINI minimizes the energy and space requirements of the device and maximizes the optical isolation and signal clarity, enabling point-of-care analysis of 96 unique samples at once. We show comparable performance to a commercial instrument using two different LAMP assays for Kaposi's sarcoma-associated herpesvirus and a common housekeeping gene, GAPDH. With a single device capable of running hundreds of samples per day, increased access to modern molecular diagnostics could improve health outcomes for a variety of diseases common in limited resource settings.
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Affiliation(s)
- Duncan McCloskey
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Juan Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher E Mason
- Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - David Erickson
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA; Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.
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