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Wilkinson AF, Barra MJ, Novak EN, Bond M, Richards-Kortum R. Point-of-care isothermal nucleic acid amplification tests: progress and bottlenecks for extraction-free sample collection and preparation. Expert Rev Mol Diagn 2024; 24:509-524. [PMID: 38973430 DOI: 10.1080/14737159.2024.2375233] [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: 12/15/2023] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION Suitable sample collection and preparation methods are essential to enable nucleic acid amplification testing at the point of care (POC). Strategies that allow direct isothermal nucleic acid amplification testing (iNAAT) of crude sample lysate without the need for nucleic acid extraction minimize time to result as well as the need for operator expertise and costly infrastructure. AREAS COVERED The authors review research to understand how sample matrix and preparation affect the design and performance of POC iNAATs. They focus on approaches where samples are directly combined with liquid reagents for preparation and amplification via iNAAT strategies. They review factors related to the type and method of sample collection, storage buffers, and lysis strategies. Finally, they discuss RNA targets and relevant regulatory considerations. EXPERT OPINION Limitations in sample preparation methods are a significant technical barrier preventing implementation of nucleic acid testing at the POC. The authors propose a framework for co-designing sample preparation and amplification steps for optimal performance with an extraction-free paradigm by considering a sample matrix and lytic strategy prior to an amplification assay and readout. In the next 5 years, the authors anticipate increasing priority on the co-design of sample preparation and iNAATs.
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Affiliation(s)
| | - Maria J Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Emilie N Novak
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Meaghan Bond
- Rice360 Institute for Global Health Technologies, Rice University, Houston, TX, USA
| | - Rebecca Richards-Kortum
- Department of Bioengineering, Rice University, Houston, TX, USA
- Rice360 Institute for Global Health Technologies, Rice University, Houston, TX, USA
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Sritong N, Sala de Medeiros M, Basing LA, Linnes JC. Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens. LAB ON A CHIP 2023; 23:888-912. [PMID: 36688463 PMCID: PMC10028599 DOI: 10.1039/d2lc00554a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | | | - Laud Anthony Basing
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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Biosensors Based on Isothermal DNA Amplification for Bacterial Detection in Food Safety and Environmental Monitoring. SENSORS 2021; 21:s21020602. [PMID: 33467078 PMCID: PMC7831002 DOI: 10.3390/s21020602] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 02/06/2023]
Abstract
The easy and rapid spread of bacterial contamination and the risk it poses to human health makes evident the need for analytical methods alternative to conventional time-consuming laboratory-based techniques for bacterial detection. To tackle this demand, biosensors based on isothermal DNA amplification methods have emerged, which avoid the need for thermal cycling, thus facilitating their integration into small and low-cost devices for in situ monitoring. This review focuses on the breakthroughs made on biosensors based on isothermal amplification methods for the detection of bacteria in the field of food safety and environmental monitoring. Optical and electrochemical biosensors based on loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), recombinase polymerase amplification (RPA), helicase dependent amplification (HDA), strand displacement amplification (SDA), and isothermal strand displacement polymerisation (ISDPR) are described, and an overview of their current advantages and limitations is provided. Although further efforts are required to harness the potential of these emerging analytical techniques, the coalescence of the different isothermal amplification techniques with the wide variety of biosensing detection strategies provides multiple possibilities for the efficient detection of bacteria far beyond the laboratory bench.
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Fowler VL, Armson B, Gonzales JL, Wise EL, Howson ELA, Vincent-Mistiaen Z, Fouch S, Maltby CJ, Grippon S, Munro S, Jones L, Holmes T, Tillyer C, Elwell J, Sowood A, de Peyer O, Dixon S, Hatcher T, Patrick H, Laxman S, Walsh C, Andreou M, Morant N, Clark D, Moore N, Houghton R, Cortes NJ, Kidd SP. A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection. J Infect 2021; 82:117-125. [PMID: 33271166 PMCID: PMC7703389 DOI: 10.1016/j.jinf.2020.10.039] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 12/23/2022]
Abstract
The COVID-19 pandemic has illustrated the importance of simple, rapid and accurate diagnostic testing. This study describes the validation of a new rapid SARS-CoV-2 RT-LAMP assay for use on extracted RNA or directly from swab offering an alternative diagnostic pathway that does not rely on traditional reagents that are often in short supply during a pandemic. Analytical specificity (ASp) of this new RT-LAMP assay was 100% and analytical sensitivity (ASe) was between 1 × 101 and 1 × 102 copies per reaction when using a synthetic DNA target. The overall diagnostic sensitivity (DSe) and specificity (DSp) of RNA RT-LAMP was 97% and 99% respectively, relative to the standard of care rRT-PCR. When a CT cut-off of 33 was employed, above which increasingly evidence suggests there is a low risk of patients shedding infectious virus, the diagnostic sensitivity was 100%. The DSe and DSp of Direct RT-LAMP (that does not require RNA extraction) was 67% and 97%, respectively. When setting CT cut-offs of ≤33 and ≤25, the DSe increased to 75% and 100%, respectively, time from swab-to-result, CT < 25, was < 15 min. We propose that RNA RT-LAMP could replace rRT-PCR where there is a need for increased sample throughput and Direct RT-LAMP as a near-patient screening tool to rapidly identify highly contagious individuals within emergency departments and care homes during times of increased disease prevalence ensuring negative results still get laboratory confirmation.
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Affiliation(s)
- Veronica L Fowler
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Eco Animal Health, The Grange, 100 The High Street, London, UK
| | - Bryony Armson
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Jose L Gonzales
- Wageningen Bioveterinary Research (WBVR), PO Box 65, 8200 AB Lelystad, the Netherlands
| | - Emma L Wise
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Emma L A Howson
- GeneSys Biotech Limited, Camberley, Surrey, UK; The Pirbright Institute, Ash Road, Pirbright, Woking, UK
| | - Zoe Vincent-Mistiaen
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Sarah Fouch
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK
| | - Connor J Maltby
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Seden Grippon
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Simon Munro
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Lisa Jones
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Tom Holmes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Claire Tillyer
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Joanne Elwell
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Amy Sowood
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Oliver de Peyer
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Sophie Dixon
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Thomas Hatcher
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Helen Patrick
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | | | | | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, UK
| | | | - Nathan Moore
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Rebecca Houghton
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Nicholas J Cortes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Stephen P Kidd
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK.
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Advances in Directly Amplifying Nucleic Acids from Complex Samples. BIOSENSORS-BASEL 2019; 9:bios9040117. [PMID: 31574959 PMCID: PMC6955841 DOI: 10.3390/bios9040117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.
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Kinoshita H, Nakamichi K, Lim CK, Takayama-Ito M, Wang L, Iizuka I, Kurane I, Saijo M. A loop-mediated isothermal amplification assay for the detection and quantification of JC polyomavirus in cerebrospinal fluid: a diagnostic and clinical management tool and technique for progressive multifocal leukoencephalopathy. Virol J 2018; 15:136. [PMID: 30170628 PMCID: PMC6119251 DOI: 10.1186/s12985-018-1046-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/20/2018] [Indexed: 01/24/2023] Open
Abstract
Background JC polyomavirus (JCV) is the causative agent of progressive multifocal leukoencephalopathy (PML), a demyelinating disease of the central nervous system in immunosuppressed patients. PML usually has a poor prognosis. Detection and quantification of the JCV genome in cerebrospinal fluid (CSF) is an efficacious tool for the diagnosis and management of PML, for which proper therapeutic interventions are required. Methods A loop-mediated isothermal amplification (LAMP) assay was applied for the quantitative detection of JCV. The LAMP assay was evaluated for the efficacy in diagnosis of PML in comparison with the TaqMan-based quantitative real-time PCR (qPCR) assay using 153 CSF specimens collected from patients with suspected PML. Results The LAMP assay showed no cross-reactivity against other polyomavirus plasmids, viral DNA, and viral RNA, which causes encephalitis, and detected 1 copy of the standard DNA per reaction. Among 50 qPCR-positives, 42 specimens (containing JCV genome ranged from 3.2 × 100 to 3.2 × 106 copies/reaction) showed positive reactions and 8 specimens (containing 0.9 to 19.9 copies/reaction) showed negative in the LAMP assay. Furthermore, 3 of 103 qPCR-negative specimens showed positive reactions in the LAMP assay. The sensitivity, specificity, positive predictive value, and negative predictive values of the LAMP assay were 84% (42/50), 97% (100/103), 93% (42/45), and 93% (100/108), respectively. The kappa statistic was 0.83. The JCV loads determined by the LAMP assay showed a strong positive correlation with those determined by the qPCR assay for 33 specimens with copy numbers of ≥1 copies/reaction (r = 0.89). Additionally, the LAMP assay could monitor the JCV genome copy number in CSF for sequential samples equivalently to qPCR assay. Conclusions The newly developed LAMP assay is highly specific against JCV and detect the JCV genome in the sample DNA containing 20 or more copies of JCV genome per reaction with 100% sensitivity (n = 29), which corresponds to ≥3 × 103 copies/mL of CSF. The LAMP assay is useful for the diagnosis and offers valuable information for the evaluation and management of PML in the clinical setting.
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Affiliation(s)
- Hitomi Kinoshita
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Kazuo Nakamichi
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Chang-Kweng Lim
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Mutsuyo Takayama-Ito
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Lixin Wang
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, 162-8640, Japan.,Present Address: School of Tropical and Laboratory, Hainan Medical University, Hainan, 571199, China
| | - Itoe Iizuka
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Ichiro Kurane
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Masayuki Saijo
- Department of Virology 1, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, 162-8640, Japan.
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Milligan JN, Shroff R, Garry DJ, Ellington AD. Evolution of a Thermophilic Strand-Displacing Polymerase Using High-Temperature Isothermal Compartmentalized Self-Replication. Biochemistry 2018; 57:4607-4619. [PMID: 29629759 DOI: 10.1021/acs.biochem.8b00200] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Strand-displacing polymerases are a crucial component of isothermal amplification (IA) reactions, where the lack of thermal cycling reduces equipment needs and improves the time to answer, especially for point-of-care applications. In order to improve the function of strand-displacing polymerases, we have developed an emulsion-based directed evolution scheme, high-temperature isothermal compartmentalized self-replication (HTI-CSR) that does not rely on thermal cycling. Starting from an algorithm-optimized shuffled library of exonuclease-deficient Family A polymerases from Geobacillus stearothermophilus (Bst LF) and Thermus aquaticus (Klentaq), we have applied HTI-CSR to generate a more thermostable strand-displacing polymerase variant that performs well in loop-mediated isothermal amplification and rolling circle amplification, even after thermal challenges of up to 95 °C that lead to better primer annealing. The new enzyme (v5.9) is also capable of a variety of new reactions, including isothermal hyperbranched rolling circle amplification. The HTI-CSR method should now prove useful for evolving additional beneficial phenotypes in strand-displacing polymerases.
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Affiliation(s)
- John N Milligan
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Daniel J Garry
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
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Mayboroda O, Katakis I, O'Sullivan CK. Multiplexed isothermal nucleic acid amplification. Anal Biochem 2018; 545:20-30. [PMID: 29353064 DOI: 10.1016/j.ab.2018.01.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/14/2022]
Abstract
Multiplexed isothermal amplification and detection of nucleic acid sequences and biomarkers is of increasing importance in diverse areas including advanced diagnostics, food quality control and environmental monitoring. Whilst there are several very elegant isothermal amplification approaches, multiplexed amplification remains a challenge, requiring careful experimental design and optimisation, from judicious primer design in order to avoid the formation of primer dimers and non-specific amplification, applied temperature as well as the ratio and concentration of primers. In this review, we describe the various approaches that have been reported to date for multiplexed isothermal amplification, for both "one-pot" multiplexing as well as parallelised multiplexing using loop-mediated isothermal amplification, strand-displacement amplification, helicase-dependent amplification, rolling circle amplification, nucleic acid sequence-based amplification, with a particular focus on recombinase polymerase amplification.
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Affiliation(s)
- Olena Mayboroda
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ioanis Katakis
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain.
| | - Ciara K O'Sullivan
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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9
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Giuffrida MC, Spoto G. Integration of isothermal amplification methods in microfluidic devices: Recent advances. Biosens Bioelectron 2017; 90:174-186. [DOI: 10.1016/j.bios.2016.11.045] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 01/02/2023]
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Martineau RL, Murray SA, Ci S, Gao W, Chao SH, Meldrum DR. Improved Performance of Loop-Mediated Isothermal Amplification Assays via Swarm Priming. Anal Chem 2016; 89:625-632. [PMID: 27809497 DOI: 10.1021/acs.analchem.6b02578] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work describes an enhancement to the loop-mediated isothermal amplification (LAMP) reaction which results in improved performance. Enhancement is achieved by adding a new set of primers to conventional LAMP reactions. These primers are termed "swarm primers" based on their relatively high concentration and their ability to create new amplicons despite the theoretical lack of single-stranded annealing sites. The primers target a region upstream of the FIP/BIP primer recognition sequences on opposite strands, substantially overlapping F1/B1 sites. Thus, despite the addition of a new primer set to an already complex assay, no significant increase in assay complexity is incurred. Swarm priming is presented for three DNA templates: Lambda phage, Synechocystis sp. PCC 6803 rbcL gene, and human HFE. The results of adding swarm primers to conventional LAMP reactions include increased amplification speed, increased indicator contrast, and increased reaction products. For at least one template, minor improvements in assay repeatability are also shown. In addition, swarm priming is shown to be effective at increasing the reaction speed for RNA amplification via RT-LAMP. Collectively, these results suggest that the addition of swarm primers will likely benefit most if not all existing LAMP assays based on state-of-the-art, six-primer reactions.
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Affiliation(s)
- Rhett L Martineau
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Sarah A Murray
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Shufang Ci
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Weimin Gao
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Shih-Hui Chao
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Deirdre R Meldrum
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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Radhika B, Kumar NV, Sreenivasulu D. Detection of Clostridium perfringens alpha toxin gene in lambs by loop mediated isothermal amplification. Vet World 2016; 9:60-4. [PMID: 27051186 PMCID: PMC4819352 DOI: 10.14202/vetworld.2016.60-64] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/02/2015] [Accepted: 12/11/2015] [Indexed: 11/16/2022] Open
Abstract
Aim: The loop mediated isothermal amplification (LAMP) was standardized for rapid detection of Clostridium perfringens. Materials and Methods: A total of 120 fecal samples were collected from enterotoxemia suspected lambs were used for screening of C. perfringens cpa gene by LAMP. The specificity of the LAMP amplified products was tested by digesting with restriction enzyme XmnI for alpha toxin gene. Results: Out of 120 samples screened 112 (93.3%) samples were positive by both LAMP and polymerase chain reaction (PCR) for detection of cpa gene which indicated the equal sensitivity of both the tests. The enzyme produced single cut in 162 base pair amplified product of alpha toxin gene at 81 base pair resulting in a single band in gel electrophoresis. Conclusion: Both LAMP and PCR for detection of cpa gene indicated the equal sensitivity of both the tests. Standardization of LAMP reaction for amplification of epsilon and beta toxin genes will help to identify the C. perfringens toxin types from the clinical samples. The test could be a suitable alternative to the PCR in detection of toxin types without the help of sophisticated machinery like thermal cycler. Considering its simplicity in operation and high sensitivity, there is the potential use of this technique in clinical diagnosis and surveillance of infectious diseases.
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Affiliation(s)
- B Radhika
- State Level Diagnostic Laboratory, College of Veterinary Science, Tirupathi, Andhra Pradesh, India
| | - N Vinod Kumar
- Department of Veterinary Microbiology, College of Veterinary Science, Tirupathi, Andhra Pradesh, India
| | - D Sreenivasulu
- Department of Veterinary Microbiology, College of Veterinary Science, Tirupathi, Andhra Pradesh, India
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12
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Ignatov KB, Barsova EV, Fradkov AF, Blagodatskikh KA, Kramarova TV, Kramarov VM. A strong strand displacement activity of thermostable DNA polymerase markedly improves the results of DNA amplification. Biotechniques 2014; 57:81-7. [PMID: 25109293 DOI: 10.2144/000114198] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 07/08/2014] [Indexed: 11/23/2022] Open
Abstract
The sensitivity and robustness of various DNA detection and amplification techniques are to a large extent determined by the properties of the DNA polymerase used. We have compared the performance of conventional Taq and Bst DNA polymerases to a novel Taq DNA polymerase mutant (SD DNA polymerase), which has a strong strand displacement activity, in PCR (including amplification of GC-rich and complex secondary structure templates), long-range PCR (LR PCR), loop-mediated amplification (LAMP), and polymerase chain displacement reaction (PCDR). Our results demonstrate that the strand displacement activity of SD DNA polymerase, in combination with the robust polymerase activity, provides a notable improvement in the sensitivity and efficiency of all these methods.
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Affiliation(s)
- Konstantin B Ignatov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; All-Russia Institute of Agricultural Biotechnology, Moscow, Russia
| | - Ekaterina V Barsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Evrogen JSC, Moscow, Russia
| | - Arkady F Fradkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Evrogen JSC, Moscow, Russia
| | | | - Tatiana V Kramarova
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vladimir M Kramarov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; All-Russia Institute of Agricultural Biotechnology, Moscow, Russia
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13
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de Paz HD, Brotons P, Muñoz-Almagro C. Molecular isothermal techniques for combating infectious diseases: towards low-cost point-of-care diagnostics. Expert Rev Mol Diagn 2014; 14:827-43. [PMID: 25052202 PMCID: PMC7103708 DOI: 10.1586/14737159.2014.940319] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nucleic acid amplification techniques such as PCR have facilitated rapid and accurate diagnosis in central laboratories over the past years. PCR-based amplifications require high-precision instruments to perform thermal cycling reactions. Such equipment is bulky, expensive and complex to operate. Progressive advances in isothermal amplification chemistries, microfluidics and detectors miniaturisation are paving the way for the introduction and use of compact ‘sample in-results out’ diagnostic devices. However, this paradigm shift towards decentralised testing poses diverse technological, economic and organizational challenges both in industrialized and developing countries. This review describes the landscape of molecular isothermal diagnostic techniques for infectious diseases, their characteristics, current state of development, and available products, with a focus on new directions towards point-of-care applications.
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Affiliation(s)
- Hector David de Paz
- Department of Molecular Microbiology, Hospital Sant Joan de Déu, University of Barcelona, Barcelona 08950, Spain
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Abstract
Effective prevention of HIV/AIDS requires early diagnosis, initiation of therapy, and regular plasma viral load monitoring of the infected individual. In addition, incidence estimation using accurate and sensitive assays is needed to facilitate HIV prevention efforts in the public health setting. Therefore, more affordable and accessible point-of-care (POC) technologies capable of providing early diagnosis, HIV viral load measurements, and CD4 counts in settings where HIV is most prevalent are needed to enable appropriate intervention strategies and ultimately stop transmission of the virus within these populations to achieve the future goal of an AIDS-free generation. This review discusses the available and emerging POC technologies for future application to these unmet public health needs.
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Sun B, Shen F, McCalla SE, Kreutz JE, Karymov MA, Ismagilov RF. Mechanistic evaluation of the pros and cons of digital RT-LAMP for HIV-1 viral load quantification on a microfluidic device and improved efficiency via a two-step digital protocol. Anal Chem 2013; 85:1540-6. [PMID: 23324061 DOI: 10.1021/ac3037206] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we used a SlipChip microfluidic device to evaluate the performance of digital reverse transcription-loop-mediated isothermal amplification (dRT-LAMP) for quantification of HIV viral RNA. Tests are needed for monitoring HIV viral load to control the emergence of drug resistance and to diagnose acute HIV infections. In resource-limited settings, in vitro measurement of HIV viral load in a simple format is especially needed, and single-molecule counting using a digital format could provide a potential solution. We showed here that when one-step dRT-LAMP is used for quantification of HIV RNA, the digital count is lower than expected and is limited by the yield of desired cDNA. We were able to overcome the limitations by developing a microfluidic protocol to manipulate many single molecules in parallel through a two-step digital process. In the first step we compartmentalize the individual RNA molecules (based on Poisson statistics) and perform reverse transcription on each RNA molecule independently to produce DNA. In the second step, we perform the LAMP amplification on all individual DNA molecules in parallel. Using this new protocol, we increased the absolute efficiency (the ratio between the concentration calculated from the actual count and the expected concentration) of dRT-LAMP 10-fold, from ∼2% to ∼23%, by (i) using a more efficient reverse transcriptase, (ii) introducing RNase H to break up the DNA:RNA hybrid, and (iii) adding only the BIP primer during the RT step. We also used this two-step method to quantify HIV RNA purified from four patient samples and found that in some cases, the quantification results were highly sensitive to the sequence of the patient's HIV RNA. We learned the following three lessons from this work: (i) digital amplification technologies, including dLAMP and dPCR, may give adequate dilution curves and yet have low efficiency, thereby providing quantification values that underestimate the true concentration. Careful validation is essential before a method is considered to provide absolute quantification; (ii) the sensitivity of dLAMP to the sequence of the target nucleic acid necessitates additional validation with patient samples carrying the full spectrum of mutations; (iii) for multistep digital amplification chemistries, such as a combination of reverse transcription with amplification, microfluidic devices may be used to decouple these steps from one another and to perform them under different, individually optimized conditions for improved efficiency.
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Affiliation(s)
- Bing Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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16
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Craw P, Balachandran W. Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review. LAB ON A CHIP 2012; 12:2469-86. [PMID: 22592150 DOI: 10.1039/c2lc40100b] [Citation(s) in RCA: 470] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.
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Affiliation(s)
- Pascal Craw
- Department of Electronic & Computer Engineering, School of Engineering & Design, Brunel University, London, UK.
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17
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Abstract
Isothermal DNA amplification is an alternative to PCR-based amplification for point-of-care diagnosis. Since the early 1990s, the approach has been refined into a simple, rapid and cost-effective tool by means of several distinct strategies. Input signals have been diversified from DNA to RNA, protein or small organic molecules by translating these signals into input DNA before amplification, thus allowing assays on various classes of biomolecules. In situ detection of single biomolecules has been achieved using an isothermal method, leveraging localized signal amplification in an intact specimen. A few pioneering studies to develop a homogenous isothermal protein assay have successfully translated structure-switching of a probe upon target binding into input DNA for isothermal amplification. In addition to the detection of specific targets, isothermal methods have made whole-genome amplification of single cells possible owing to the unbiased, linear nature of the amplification process as well as the large size of amplified products given by ϕ29 DNA polymerase. These applications have been devised with the four isothermal amplification strategies covered in this review: strand-displacement amplification, rolling circle amplification, helicase-dependent amplification and recombinase polymerase amplification.
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NEMOTO M, OHTA M, TSUJIMURA K, BANNAI H, YAMANAKA T, KONDO T, MATSUMURA T. Direct Detection of Equine Herpesvirus Type 1 DNA in Nasal Swabs by Loop-Mediated Isothermal Amplification (LAMP). J Vet Med Sci 2011; 73:1225-7. [DOI: 10.1292/jvms.11-0065] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Manabu NEMOTO
- Epizootic Research Center, Equine Research Institute, Japan Racing Association
| | - Minoru OHTA
- Racehorse Clinic, Ritto Training Center, Japan Racing Association
| | - Koji TSUJIMURA
- Epizootic Research Center, Equine Research Institute, Japan Racing Association
| | - Hiroshi BANNAI
- Epizootic Research Center, Equine Research Institute, Japan Racing Association
| | - Takashi YAMANAKA
- Epizootic Research Center, Equine Research Institute, Japan Racing Association
| | - Takashi KONDO
- Epizootic Research Center, Equine Research Institute, Japan Racing Association
| | - Tomio MATSUMURA
- Epizootic Research Center, Equine Research Institute, Japan Racing Association
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Geojith G, Dhanasekaran S, Chandran SP, Kenneth J. Efficacy of loop mediated isothermal amplification (LAMP) assay for the laboratory identification of Mycobacterium tuberculosis isolates in a resource limited setting. J Microbiol Methods 2010; 84:71-3. [PMID: 21047534 DOI: 10.1016/j.mimet.2010.10.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 10/05/2010] [Accepted: 10/21/2010] [Indexed: 10/18/2022]
Abstract
Current methods of TB diagnosis are time consuming and less suited for developing countries. The LAMP (loop mediated isothermal amplification) is a rapid method more suitable for diagnosis in resource limited settings and has been proposed as a viable test requiring further evaluation for use as a laboratory method as well. We evaluated two LAMP assays, using culture lysates of clinical sputum samples (from Southern India) and compared it to a proprietary multiplex PCR reverse-hybridization line probe assay ('GenoType MTBC' from HAIN Lifescience GmbH, Germany). The LAMP procedure was modified to suit the local conditions. The Mycobacterium tuberculosis specific LAMP assay ('MTB LAMP') showed sensitivity and specificity, of 44.7% and 94.4% respectively in a 60 min format, 85.7% and 93.9% respectively in a 90 min format and 91.7%, and 90.9% respectively in a 120 min format. The Mycobacteria universal LAMP assay ('Muniv LAMP') showed a sensitivity of 99.1%. The LAMP was shown to be a rapid and accessible assay for the laboratory identification of M. tuberculosis isolates. Initial denaturation of template was shown to be essential for amplification in unpurified/dilute samples and longer incubation was shown to increase the sensitivity. The need for modification of protocols to yield better efficacy in this scenario needs to be addressed in subsequent studies.
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Affiliation(s)
- G Geojith
- Infectious disease unit, St. John's Research Institute, Bangalore, India
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