1
|
Natsuhara D, Miyajima A, Bussho T, Okamoto S, Nagai M, Ihira M, Shibata T. A microfluidic-based quantitative analysis system for the multiplexed genetic diagnosis of human viral infections using colorimetric loop-mediated isothermal amplification. Analyst 2024; 149:3335-3345. [PMID: 38695841 DOI: 10.1039/d4an00215f] [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: 06/11/2024]
Abstract
In this study, a microfluidic-based system utilizing colorimetric loop-mediated isothermal amplification (LAMP) is introduced for the quantitative analysis of nucleic acid targets. This system offers a user-friendly and cost-effective platform for the multiplexed genetic diagnosis of various infectious diseases across multiple samples. It includes time-lapse imaging equipment for capturing images of the microfluidic device during the LAMP assay and a hue-based quantitative analysis software to analyze the LAMP reaction, streamlining diagnostic procedures. An electric pipette was used to simplify the loading of samples and LAMP reagents into the device, allowing easy operation even by untrained individuals. The hue-based analysis software employs efficient image processing and post-processing techniques to calculate DNA amplification curves based on color changes in multiple reaction chambers. This software automates several tasks, such as identifying reaction chamber areas from time-lapse images, quantifying color information within each chamber, correcting baselines of DNA amplification curves, fitting experimental data to theoretical curves, and determining the threshold time for each curve. To validate the developed system, conventional off-chip LAMP assays were conducted with a 25 μL reaction mixture in 0.2 mL polymerase chain reaction (PCR) tubes using a real-time turbidimeter. The results indicated that the threshold time obtained using the colorimetric LAMP assay in the developed system is comparable to that obtained with real-time turbidity measurements in PCR tubes, demonstrating the system's capability for quantitative analysis of target nucleic acids, including those from human herpesviruses.
Collapse
Affiliation(s)
- Daigo Natsuhara
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Akira Miyajima
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Tomoya Bussho
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Shunya Okamoto
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
- Institute for Research on Next-generation Semiconductor and Sensing Science (IRES2), Toyohashi University of Technology, Aichi 441-8580, Japan
| | - Masaru Ihira
- Faculty of Clinical Science for Biological Monitoring, Fujita Health University, Aichi 470-1192, Japan
| | - Takayuki Shibata
- Department of Mechanical Engineering, Toyohashi University of Technology, Aichi 441-8580, Japan.
| |
Collapse
|
2
|
Chen X, Du C, Zhao Q, Zhao Q, Wan Y, He J, Yuan W. Rapid and visual identification of HIV-1 using reverse transcription loop-mediated isothermal amplification integrated with a gold nanoparticle-based lateral flow assay platform. Front Microbiol 2023; 14:1230533. [PMID: 37502395 PMCID: PMC10368893 DOI: 10.3389/fmicb.2023.1230533] [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: 05/29/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Human immunodeficiency virus type one (HIV-1) infection remains a major public health problem worldwide. Early diagnosis of HIV-1 is crucial to treat and control this infection effectively. Here, for the first time, we reported a novel molecular diagnostic assay called reverse transcription loop-mediated isothermal amplification combined with a visual gold nanoparticle-based lateral flow assay (RT-LAMP-AuNPs-LFA), which we devised for rapid, specific, sensitive, and visual identification of HIV-1. The unique LAMP primers were successfully designed based on the pol gene from the major HIV-1 genotypes CRF01_AE, CRF07_BC, CRF08_BC, and subtype B, which are prevalent in China. The optimal HIV-1-RT-LAMP-AuNPs-LFA reaction conditions were determined to be 68°C for 35 min. The detection procedure, including crude genomic RNA isolation (approximately 5 min), RT-LAMP amplification (35 min), and visual result readout (<2 min), can be completed within 45 min. Our assay has a detection limit of 20 copies per test, and we did not observe any cross-reactivity with any other pathogen in our testing. Hence, our preliminary results indicated that the HIV-1-RT-LAMP-AuNPs-LFA assay can potentially serve as a useful point-of-care diagnostic tool for HIV-1 detection in a clinical setting.
Collapse
Affiliation(s)
- Xu Chen
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- Clinical Medical Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Cheng Du
- Department of Anesthesiology, The Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Qiang Zhao
- Clinical Laboratory, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
| | - Qi Zhao
- Gastroenterology of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Yonghu Wan
- Experiment Center, Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Jun He
- Clinical Laboratory, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
| | - Wei Yuan
- Department of Quality Control, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
| |
Collapse
|
3
|
Gulinaizhaer A, Zou M, Ma S, Yao Y, Fan X, Wu G. Isothermal nucleic acid amplification technology in HIV detection. Analyst 2023; 148:1189-1208. [PMID: 36825492 DOI: 10.1039/d2an01813f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nucleic acid testing for HIV plays an important role in the early diagnosis and monitoring of antiretroviral therapy outcomes in HIV patients and HIV-infected infants. Currently, the main molecular diagnostic methods employed are complex, time-consuming, and expensive to operate in resource-limited areas. Isothermal nucleic acid amplification technology overcomes some of the shortcomings of traditional assays and makes it possible to use point-of-care tests for molecular HIV detection. Here, we summarize and discuss the latest technological advances in isothermal nucleic acid amplification for HIV detection, with the intent of providing guidance for the development of subsequent HIV assays with high sensitivity and specificity.
Collapse
Affiliation(s)
- Abudushalamu Gulinaizhaer
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Mingyuan Zou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Shuo Ma
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Yuming Yao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Xiaobo Fan
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China. .,Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing 210009, Jiangsu, China
| |
Collapse
|
4
|
Li X, Wang J, Geng J, Xiao L, Wang H. Emerging Landscape of SARS-CoV-2 Variants and Detection Technologies. Mol Diagn Ther 2023; 27:159-177. [PMID: 36577887 PMCID: PMC9797111 DOI: 10.1007/s40291-022-00631-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2022] [Indexed: 12/29/2022]
Abstract
In 2019, a new coronavirus was identified that has caused significant morbidity and mortality worldwide. Like all RNA viruses, severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) evolves over time through random mutation resulting in genetic variations in the population. Although the currently approved coronavirus disease 2019 vaccines can be given to those over 5 years of age and older in most countries, strikingly, the number of people diagnosed positive for SARS-Cov-2 is still increasing. Therefore, to prevent and control this epidemic, early diagnosis of infected individuals is of great importance. The current detection of SARS-Cov-2 coronavirus variants are mainly based on reverse transcription-polymerase chain reaction. Although the sensitivity of reverse transcription-polymerase chain reaction is high, it has some disadvantages, for example, multiple temperature changes, long detection time, complicated operation, expensive instruments, and the need for professional personnel, which brings considerable inconvenience to the early diagnosis of this virus. This review comprehensively summarizes the development and application of various current detection technologies for novel coronaviruses, including isothermal amplification, CRISPR-Cas detection, serological detection, biosensor, ensemble, and microfluidic technology, along with next-generation sequencing. Those findings offer us a great potential to replace or combine with reverse transcription-polymerase chain reaction detection to achieve the purpose of allowing predictive diagnostics and targeted prevention of SARS-Cov-2 in the future.
Collapse
Affiliation(s)
- Xianghui Li
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China
| | - Jing Wang
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jingping Geng
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China
| | - Liming Xiao
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Hu Wang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang, 443002, China.
- Institute of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
5
|
Bacon A, Wang W, Lee H, Umrao S, Sinawang PD, Akin D, Khemtonglang K, Tan A, Hirshfield S, Demirci U, Wang X, Cunningham BT. Review of HIV Self Testing Technologies and Promising Approaches for the Next Generation. BIOSENSORS 2023; 13:298. [PMID: 36832064 PMCID: PMC9954708 DOI: 10.3390/bios13020298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 05/28/2023]
Abstract
The ability to self-test for HIV is vital to preventing transmission, particularly when used in concert with HIV biomedical prevention modalities, such as pre-exposure prophylaxis (PrEP). In this paper, we review recent developments in HIV self-testing and self-sampling methods, and the potential future impact of novel materials and methods that emerged through efforts to develop more effective point-of-care (POC) SARS-CoV-2 diagnostics. We address the gaps in existing HIV self-testing technologies, where improvements in test sensitivity, sample-to-answer time, simplicity, and cost are needed to enhance diagnostic accuracy and widespread accessibility. We discuss potential paths toward the next generation of HIV self-testing through sample collection materials, biosensing assay techniques, and miniaturized instrumentation. We discuss the implications for other applications, such as self-monitoring of HIV viral load and other infectious diseases.
Collapse
Affiliation(s)
- Amanda Bacon
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weijing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hankeun Lee
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Saurabh Umrao
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
| | - Prima Dewi Sinawang
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Demir Akin
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
- Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD), School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kodchakorn Khemtonglang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anqi Tan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sabina Hirshfield
- Special Treatment and Research (STAR) Program, Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, New York, NY 11203, USA
| | - Utkan Demirci
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Xing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brian T. Cunningham
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
| |
Collapse
|
6
|
Khan MJR, Bhuiyan MA, Tabassum S, Munshi SU. Use of whole blood and dried blood spot for detection of HIV-1 nucleic acids using reverse transcription loop-mediated isothermal amplification. J Virol Methods 2023; 312:114642. [PMID: 36375538 DOI: 10.1016/j.jviromet.2022.114642] [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: 07/06/2022] [Revised: 10/15/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]
Abstract
For monitoring viral load (VL) or Early Infant Diagnosis (EID) of HIV-1, real-time Polymerase Chain Reaction (qPCR) is used to perform on plasma or Dried Blood Spot (DBS) sample. The qPCR method is expensive and requires sophisticated equipment. Therefore, there is a requirement for newer and cheaper technology for VL measurement or EID. In this analytical study, a Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) assay was optimized and applied for amplification of HIV nucleic acids (NA) extracted from plasma, heat-treated plasma, heat-treated whole blood and lysis buffer-treated dried blood spot (DBS). The amplified product of RT-LAMP assay was detected by color change of Hydroxy naphthol blue (HNB) dye, step ladder pattern band on agarose gel after electrophoresis and sigmoid-shaped curve in the real-time thermal cycler. Comparing the results from RT-LAMP testing of all conditions with the results obtained by RT-qPCR results, viewed as the gold standard; a relative analytical sensitivity and specificity of RT-LAMP was calculated as 100 % and 90 % respectively. The corresponding positive predictive value (PPV) and negative predictive value (NPV) were 93.75 % and 100 %, respectively. The percentage of agreement between the RT-LAMP and RT-qPCR was 88.46% and Cohen's kappa value was 0.75 shows a substantial agreement between the two tests. This study suggests that whole blood or DBS may be useful specimens for analysis by HIV-1 specific RT-LAMP, to provide a cost effective alternative to RT-qPCR for the detection of HIV-1 nucleic acid at the point of care, or in early infant diagnoses.
Collapse
|
7
|
Matute T, Nuñez I, Rivera M, Reyes J, Blázquez-Sánchez P, Arce A, Brown AJ, Gandini C, Molloy J, Ramírez-Sarmiento CA, Federici F. Homebrew reagents for low-cost RT-LAMP. J Biomol Tech 2021; 32:114-120. [PMID: 35027869 PMCID: PMC8730520 DOI: 10.7171/jbt.21-3203-006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
Abstract
Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) has gained popularity for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The high specificity, sensitivity, simple protocols, and potential to deliver results without the use of expensive equipment has made it an attractive alternative to RT-PCR. However, the high cost per reaction, the centralized manufacturing of required reagents, and their distribution under cold chain shipping limit RT-LAMP's applicability in low-income settings. The preparation of assays using homebrew enzymes and buffers has emerged worldwide as a response to these limitations and potential shortages. Here, we describe the production of Moloney murine leukemia virus reverse transcriptase and BstLF DNA polymerase for the local implementation of RT-LAMP reactions at low cost. These reagents compared favorably to commercial kits, and optimum concentrations were defined in order to reduce time to threshold, increase ON/OFF range, and minimize enzyme quantities per reaction. As a validation, we tested the performance of these reagents in the detection of SARS-CoV-2 from RNA extracted from clinical nasopharyngeal samples, obtaining high agreement between RT-LAMP and RT-PCR clinical results. The in-house preparation of these reactions results in an order of magnitude reduction in costs; thus, we provide protocols and DNA to enable the replication of these tests at other locations. These results contribute to the global effort of developing open and low-cost diagnostics that enable technological autonomy and distributed capacities in viral surveillance.
Collapse
Affiliation(s)
- Tamara Matute
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maira Rivera
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Reyes
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aníbal Arce
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexander J. Brown
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chiara Gandini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - César A. Ramírez-Sarmiento
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| |
Collapse
|
8
|
Matute T, Nuñez I, Rivera M, Reyes J, Blázquez-Sánchez P, Arce A, Brown AJ, Gandini C, Molloy J, Ramirez-Sarmiento CA, Federici F. Homebrew reagents for low cost RT-LAMP. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.08.21256891. [PMID: 34013302 PMCID: PMC8132288 DOI: 10.1101/2021.05.08.21256891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
RT-LAMP (reverse transcription - Loop-mediated isothermal amplification) has gained popularity for the detection of SARS-CoV-2. The high specificity, sensitivity, simple protocols and potential to deliver results without the use of expensive equipment has made it an attractive alternative to RT-PCR. However, the high cost per reaction, the centralized manufacturing of required reagents and their distribution under cold chain shipping limits RT-LAMP's applicability in low-income settings. The preparation of assays using homebrew enzymes and buffers has emerged worldwide as a response to these limitations and potential shortages. Here, we describe the production of Moloney murine leukemia virus (M-MLV) Reverse Transcriptase and BstLF DNA polymerase for the local implementation of RT-LAMP reactions at low cost. These reagents compared favorably to commercial kits and optimum concentrations were defined in order to reduce time to threshold, increase ON/OFF range and minimize enzyme quantities per reaction. As a validation, we tested the performance of these reagents in the detection of SARS-CoV-2 from RNA extracted from clinical nasopharyngeal samples, obtaining high agreement between RT-LAMP and RT-PCR clinical results. The in-house preparation of these reactions results in an order of magnitude reduction in costs, and thus we provide protocols and DNA to enable the replication of these tests at other locations. These results contribute to the global effort of developing open and low cost diagnostics that enable technological autonomy and distributed capacities in viral surveillance.
Collapse
Affiliation(s)
- Tamara Matute
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maira Rivera
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Reyes
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Aníbal Arce
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexander J. Brown
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Chiara Gandini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - César A. Ramirez-Sarmiento
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation. Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
9
|
Augustine R, Hasan A, Das S, Ahmed R, Mori Y, Notomi T, Kevadiya BD, S. Thakor A. Loop-Mediated Isothermal Amplification (LAMP): A Rapid, Sensitive, Specific, and Cost-Effective Point-of-Care Test for Coronaviruses in the Context of COVID-19 Pandemic. BIOLOGY 2020; 9:E182. [PMID: 32707972 PMCID: PMC7464797 DOI: 10.3390/biology9080182] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
The rampant spread of COVID-19 and the worldwide prevalence of infected cases demand a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. The most common molecular tests approved by regulatory bodies across the world for COVID-19 diagnosis are based on Polymerase Chain Reaction (PCR). While PCR-based tests are highly sensitive, specific, and remarkably reliable, they have many limitations ranging from the requirement of sophisticated laboratories, need of skilled personnel, use of complex protocol, long wait times for results, and an overall high cost per test. These limitations have inspired researchers to search for alternative diagnostic methods that are fast, economical, and executable in low-resource laboratory settings. The discovery of Loop-mediated isothermal Amplification (LAMP) has provided a reliable substitute platform for the accurate detection of low copy number nucleic acids in the diagnosis of several viral diseases, including epidemics like Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). At present, a cocktail of LAMP assay reagents along with reverse transcriptase enzyme (Reverse Transcription LAMP, RT-LAMP) can be a robust solution for the rapid and cost-effective diagnosis for COVID-19, particularly in developing, and low-income countries. In summary, the development of RT-LAMP based diagnostic tools in a paper/strip format or the integration of this method into a microfluidic platform such as a Lab-on-a-chip may revolutionize the concept of PoCT for COVID-19 diagnosis. This review discusses the principle, technology and past research underpinning the success for using this method for diagnosing MERS and SARS, in addition to ongoing research, and the prominent prospect of RT-LAMP in the context of COVID-19 diagnosis.
Collapse
Affiliation(s)
- Robin Augustine
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Suvarthi Das
- Department of Medicine, Stanford University Medical Center, Palo Alto, CA 94304, USA;
| | - Rashid Ahmed
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Yasuyoshi Mori
- Eiken Chemical Co., Ltd., Research and Development Division, Taito-ku 110-8408, Japan; (Y.M.); (T.N.)
| | - Tsugunori Notomi
- Eiken Chemical Co., Ltd., Research and Development Division, Taito-ku 110-8408, Japan; (Y.M.); (T.N.)
| | - Bhavesh D. Kevadiya
- Interventional Regenerative Medicine and Imaging Laboratory, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; (B.D.K.); (A.S.T.)
| | - Avnesh S. Thakor
- Interventional Regenerative Medicine and Imaging Laboratory, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; (B.D.K.); (A.S.T.)
| |
Collapse
|
10
|
Curtis KA, Morrison D, Rudolph DL, Shankar A, Bloomfield LSP, Switzer WM, Owen SM. A multiplexed RT-LAMP assay for detection of group M HIV-1 in plasma or whole blood. J Virol Methods 2018; 255:91-97. [PMID: 29474813 DOI: 10.1016/j.jviromet.2018.02.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/24/2022]
Abstract
Isothermal nucleic acid amplification techniques, such as reverse-transcription loop-mediated isothermal amplification (RT-LAMP), exhibit characteristics that are suitable for the development of a rapid, low-cost NAT that can be used at the POC. For demonstration of utility for global use, studies are needed to validate the performance of RT-LAMP for the detection of divergent subtypes. In this study, we designed and evaluated multiplexed HIV-1 integrase RT-LAMP primers to detect subtypes within group M, along with an RNase P positive internal processing and amplification control. Using a panel of 26 viral isolates representing the major circulating subtypes, we demonstrated detection of all isolates of subtypes A1, C, D, F1, F2, G, CRF01_AE, CRF02_AG, and two unique recombinant forms (URFs). A whole blood panel created with one representative isolate of each subtype was successfully amplified with the group M HIV-1 integrase and RNase P internal control primers. The group M HIV-1 RT-LAMP assay was further evaluated on 61 plasma specimens obtained from persons from Cameroon and Uganda. The sequence-conserved group M HIV-1 RT-LAMP primers, coupled to a low-cost amplification device, may improve diagnosis of acute infection at the POC and provide timely confirmation of HIV status.
Collapse
Affiliation(s)
- Kelly A Curtis
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Daphne Morrison
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Donna L Rudolph
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Laura S P Bloomfield
- Stanford University School of Medicine, Stanford, CA, USA; Emmett Interdisciplinary Program in Environment and Resources, Stanford, CA, USA
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - S Michele Owen
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
11
|
Mauk M, Song J, Bau HH, Gross R, Bushman FD, Collman RG, Liu C. Miniaturized devices for point of care molecular detection of HIV. LAB ON A CHIP 2017; 17:382-394. [PMID: 28092381 PMCID: PMC5285266 DOI: 10.1039/c6lc01239f] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The HIV pandemic affects 36.7 million people worldwide, predominantly in resource-poor settings. Nucleic acid-based molecular detection of HIV plays a significant role in antiretroviral treatment monitoring for HIV patients, as well as diagnosis of HIV infection in infants. Currently available molecular diagnostic methods are complex, time-consuming and relatively expensive, thus limiting their use in resource-poor settings. Recent advances in microfluidics technology have made possible low-cost integrated miniaturized devices for molecular detection and quantification of HIV at the point of care. We review recent technical advances in molecular testing of HIV using microfluidic technology, with a focus on assays based on isothermal nucleic acid amplification. Microfluidic components for sample preparation, isothermal amplification and result detection are discussed and compared. We also discuss the challenges and future directions for developing an integrated "sample-to-result" microfluidic platform for HIV molecular detection.
Collapse
Affiliation(s)
- Michael Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Robert Gross
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| |
Collapse
|
12
|
Xu G, Gunson RN, Cooper JM, Reboud J. Rapid ultrasonic isothermal amplification of DNA with multiplexed melting analysis – applications in the clinical diagnosis of sexually transmitted diseases. Chem Commun (Camb) 2015; 51:2589-92. [PMID: 25569801 DOI: 10.1039/c4cc08389j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a nucleic acid testing (NAT) platform for infectious disease diagnostics at the point-of-care, using surface acoustic waves (SAW) to perform a multiplexed loop-mediated isothermal amplification (LAMP) test for sexually transmitted diseases. The ultrasonic actuation not only enables faster NAT reactions but also provides a route towards integrating low-cost, low-power molecular diagnostics into disposable sensors.
Collapse
Affiliation(s)
- Gaolian Xu
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Rankine Building, G12 8LT Glasgow, UK.
| | | | | | | |
Collapse
|
13
|
Abdullah J, Saffie N, Sjasri FAR, Husin A, Abdul-Rahman Z, Ismail A, Aziah I, Mohamed M. Rapid detection of Salmonella Typhi by loop-mediated isothermal amplification (LAMP) method. Braz J Microbiol 2015; 45:1385-91. [PMID: 25763045 PMCID: PMC4323314 DOI: 10.1590/s1517-83822014000400032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 04/17/2014] [Indexed: 11/21/2022] Open
Abstract
An in-house loop-mediated isothermal amplification (LAMP) reaction was established and evaluated for sensitivity and specificity in detecting the presence of Salmonella Typhi (S. Typhi) isolates from Kelantan, Malaysia. Three sets of primers consisting of two outer and 4 inner were designed based on locus STBHUCCB_38510 of chaperone PapD of S. Typhi genes. The reaction was optimised using genomic DNA of S. Typhi ATCC7251 as the template. The products were visualised directly by colour changes of the reaction. Positive results were indicated by green fluorescence and negative by orange colour. The test was further evaluated for specificity, sensitivity and application on field samples. The results were compared with those obtained by gold standard culture method and Polymerase Chain Reaction (PCR). This method was highly specific and -10 times more sensitive in detecting S. Typhi compared to the optimised conventional polymerase chain reaction (PCR) method.
Collapse
Affiliation(s)
- J Abdullah
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - N Saffie
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - F A R Sjasri
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - A Husin
- Hospital Raja Perempuan Zainab II 15586 Kota BharuKelantan Malaysia Hospital Raja Perempuan Zainab II, 15586 Kota Bharu, Kelantan, Malaysia
| | - Z Abdul-Rahman
- School of Medical Sciences Universiti Sains Malaysia Kubang Kerian Kelantan School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan
| | - A Ismail
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - I Aziah
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - M Mohamed
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| |
Collapse
|
14
|
Ocwieja KE, Sherrill-Mix S, Liu C, Song J, Bau H, Bushman FD. A reverse transcription loop-mediated isothermal amplification assay optimized to detect multiple HIV subtypes. PLoS One 2015; 10:e0117852. [PMID: 25675344 PMCID: PMC4326360 DOI: 10.1371/journal.pone.0117852] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/04/2015] [Indexed: 11/18/2022] Open
Abstract
Diagnostic methods for detecting and quantifying HIV RNA have been improving, but efficient methods for point-of-care analysis are still needed, particularly for applications in resource-limited settings. Detection based on reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is particularly useful for this, because when combined with fluorescence-based DNA detection, RT-LAMP can be implemented with minimal equipment and expense. Assays have been developed to detect HIV RNA with RT-LAMP, but existing methods detect only a limited subset of HIV subtypes. Here we report a bioinformatic study to develop optimized primers, followed by empirical testing of 44 new primer designs. One primer set (ACeIN-26), targeting the HIV integrase coding region, consistently detected subtypes A, B, C, D, and G. The assay was sensitive to at least 5000 copies per reaction for subtypes A, B, C, D, and G, with Z-factors of above 0.69 (detection of the minor subtype F was found to be unreliable). There are already rapid and efficient assays available for detecting HIV infection in a binary yes/no format, but the rapid RT-LAMP assay described here has additional uses, including 1) tracking response to medication by comparing longitudinal values for a subject, 2) detecting of infection in neonates unimpeded by the presence of maternal antibody, and 3) detecting infection prior to seroconversion.
Collapse
Affiliation(s)
- Karen E. Ocwieja
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Haim Bau
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
15
|
Electricity-free amplification and detection for molecular point-of-care diagnosis of HIV-1. PLoS One 2014; 9:e113693. [PMID: 25426953 PMCID: PMC4245218 DOI: 10.1371/journal.pone.0113693] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 10/28/2014] [Indexed: 11/28/2022] Open
Abstract
In resource-limited settings, the lack of decentralized molecular diagnostic testing and sparse access to centralized medical facilities can present a critical barrier to timely diagnosis, treatment, and subsequent control and elimination of infectious diseases. Isothermal nucleic acid amplification methods, including reverse transcription loop-mediated isothermal amplification (RT-LAMP), are well-suited for decentralized point-of-care molecular testing in minimal infrastructure laboratories since they significantly reduce the complexity of equipment and power requirements. Despite reduced complexity, however, there is still a need for a constant heat source to enable isothermal nucleic acid amplification. This requirement poses significant challenges for laboratories in developing countries where electricity is often unreliable or unavailable. To address this need, we previously developed a low-cost, electricity-free heater using an exothermic reaction thermally coupled with a phase change material. This heater achieved acceptable performance, but exhibited considerable variability. Furthermore, as an enabling technology, the heater was an incomplete diagnostic solution. Here we describe a more precise, affordable, and robust heater design with thermal standard deviation <0.5°C at operating temperature, a cost of approximately US$.06 per test for heater reaction materials, and an ambient temperature operating range from 16°C to 30°C. We also pair the heater with nucleic acid lateral flow (NALF)-detection for a visual readout. To further illustrate the utility of the electricity-free heater and NALF-detection platform, we demonstrate sensitive and repeatable detection of HIV-1 with a ß-actin positive internal amplification control from processed sample to result in less than 80 minutes. Together, these elements are building blocks for an electricity-free platform capable of isothermal amplification and detection of a variety of pathogens.
Collapse
|
16
|
Odari EO, Maiyo A, Lwembe R, Gurtler L, Eberle J, Nitschko H. Establishment and evaluation of a loop-mediated isothermal amplification (LAMP) assay for the semi-quantitative detection of HIV-1 group M virus. J Virol Methods 2014; 212:30-8. [PMID: 25445795 DOI: 10.1016/j.jviromet.2014.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/29/2014] [Accepted: 10/28/2014] [Indexed: 10/24/2022]
Abstract
The past decade has witnessed a dramatic increase of anti-retroviral treatment of human immunodeficiency virus (HIV) infected patients in many African countries. Due to costs and lack of currently available commercial viral load assays, insufficient attention has been paid to therapy monitoring through measurement of plasma viral load. This challenge of patient monitoring by tests as viral load, CD4 cell count, and finally HIV drug resistance could reverse achievements already made against HIV/AIDS infection. Loop-mediated isothermal amplification (LAMP) has been shown to be simple, rapid and cost-effective, characteristics which make this assay suitable for viral load monitoring in resource limited settings. This paper describes a revised LAMP assay using primers in the HIV-1 integrase region. The assay can be used for semi-quantitative measurement of HIV-1 group M viral load. The lower limit of detection (LLOD) was determined as 1200copies/mL and lower limit of quantitation (LLOQ) at 9800copies/mL. Sensitivities of 82 and 86% (in 135 and 99 plasma samples respectively from Kenya) and 93% (in 112 plasma samples from Germany) and specificities of 99 and 100% were realized. HIV-1 group O and HIV-2 virus samples were not detected. This LAMP assay has the potential for semi-quantitation of HIV-1 group M viral load in resource limited countries. There is still a need for further improvement by refinement of primers in respect to detection of HIV-1 group M non-B virus.
Collapse
Affiliation(s)
- Eddy Okoth Odari
- Max von Pettenkofer-Institute for Hygiene and Medical Microbiology (MVPI), Ludwig-Maximilians-University, Pettenkofer Strasse 9a, 80336 Munich, Germany; Center for International Health (CIH) at the Ludwig-Maximilians-University, Leopoldstraße 7, 80802 Munich, Germany; Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62 000, 00200 Nairobi, Kenya.
| | - Alex Maiyo
- Kenya Medical Research Institute (KEMRI), Mbagathi, P.O. Box 54840, Nairobi, Kenya
| | - Raphael Lwembe
- Kenya Medical Research Institute (KEMRI), Mbagathi, P.O. Box 54840, Nairobi, Kenya
| | - Lutz Gurtler
- Max von Pettenkofer-Institute for Hygiene and Medical Microbiology (MVPI), Ludwig-Maximilians-University, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Josef Eberle
- Max von Pettenkofer-Institute for Hygiene and Medical Microbiology (MVPI), Ludwig-Maximilians-University, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Hans Nitschko
- Max von Pettenkofer-Institute for Hygiene and Medical Microbiology (MVPI), Ludwig-Maximilians-University, Pettenkofer Strasse 9a, 80336 Munich, Germany
| |
Collapse
|
17
|
Zeng Y, Zhang X, Nie K, Ding X, Ring BZ, Xu L, Dai L, Li X, Ren W, Shi L, Ma X. Rapid quantitative detection of Human immunodeficiency virus type 1 by a reverse transcription-loop-mediated isothermal amplification assay. Gene 2014; 541:123-8. [PMID: 24630968 DOI: 10.1016/j.gene.2014.03.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 02/13/2014] [Accepted: 03/07/2014] [Indexed: 11/28/2022]
Abstract
Accurate and rapid quantitation of Human immunodeficiency virus type 1 (HIV-1) RNA levels is a critical aspect in estimating the effect of antiviral therapy and establishing therapeutic schedule. Thus, for the first time, a rapid quantitative reverse transcription-loop-mediated isothermal amplification (RT-LAMP) was designed to quantitate HIV-1 RNA. The results showed that the dynamic range was from 2.5×10(2) to 10(7) copies with a coefficient of determination (R(2)) of 0.991, and the limit of detection of RT-LAMP by Probit analysis at the 95% detection level was 196 copies. The intra-assay coefficient of variation (CV) ranged from 0.67% to 2.08% at 10(7) copies and 7.25% to 12.97% at 250 copies. The CVs of inter-assay were 2.39% and 13.93% for the high and low copy numbers, respectively. No cross-reaction with Human immunodeficiency virus type 2 (HIV-2), Human T lymphotrophic virus type 1 (HTLV-1) and Hepatitis C virus (HCV) was observed and a good agreement between the RT-LAMP method and the real-time reverse transcription-polymerase chain reaction (qRT-PCR) test was achieved. This proposed RT-LAMP method could be useful for rapid diagnosis of high risk group and pharmacodynamic assessment of anti-HIV drug, especially in less-equipped laboratories of impoverished areas.
Collapse
Affiliation(s)
- Yalan Zeng
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Xiaoguang Zhang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kai Nie
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiong Ding
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Brian Z Ring
- Institute of Genomic and Personalized Medicine, School of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Lanying Xu
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Lei Dai
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Xiying Li
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Wei Ren
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Lei Shi
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China.
| | - Xuejun Ma
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| |
Collapse
|
18
|
Salar R, Gahlawat S, Siwach P, Duhan J, Gahlawat SK. Rapid Detection of Viruses Using Loop-Mediated Isothermal Amplification (LAMP): A Review. BIOTECHNOLOGY: PROSPECTS AND APPLICATIONS 2013. [PMCID: PMC7122297 DOI: 10.1007/978-81-322-1683-4_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most of the diseases caused by viral infection are found to be fatal, and the diagnosis is difficult due to confusion with other causative agents. So, a highly efficient molecular-based advance detection technique, i.e., loop-mediated isothermal amplification (LAMP) method, is developed for diagnosis of viral infections by various workers. It is based on amplification of DNA at very low level under isothermal conditions, using a set of four specifically designed primers and a DNA polymerase with strand displacement activity. This technique is found to be superior than most of the molecular techniques like PCR, RT-PCR, and real-time PCR due to its high specificity, sensitivity, and rapidity. Major advantage of LAMP method is its cost-effectiveness as it can be done simply by using water bath or dry bath. Here, in this review information regarding almost all the effective LAMP techniques which is developed so far for diagnosis of numerous viral pathogens is presented.
Collapse
Affiliation(s)
- R.K. Salar
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - S.K. Gahlawat
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - P. Siwach
- grid.448811.0Department of Biotechnology, Chaudhary Devi lal University, Sirsa, Haryana India
| | - J.S. Duhan
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | | |
Collapse
|
19
|
Myers FB, Henrikson RH, Bone J, Lee LP. A handheld point-of-care genomic diagnostic system. PLoS One 2013; 8:e70266. [PMID: 23936402 PMCID: PMC3731356 DOI: 10.1371/journal.pone.0070266] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 06/18/2013] [Indexed: 11/18/2022] Open
Abstract
The rapid detection and identification of infectious disease pathogens is a critical need for healthcare in both developed and developing countries. As we gain more insight into the genomic basis of pathogen infectivity and drug resistance, point-of-care nucleic acid testing will likely become an important tool for global health. In this paper, we present an inexpensive, handheld, battery-powered instrument designed to enable pathogen genotyping in the developing world. Our Microfluidic Biomolecular Amplification Reader (µBAR) represents the convergence of molecular biology, microfluidics, optics, and electronics technology. The µBAR is capable of carrying out isothermal nucleic acid amplification assays with real-time fluorescence readout at a fraction of the cost of conventional benchtop thermocyclers. Additionally, the µBAR features cell phone data connectivity and GPS sample geotagging which can enable epidemiological surveying and remote healthcare delivery. The µBAR controls assay temperature through an integrated resistive heater and monitors real-time fluorescence signals from 60 individual reaction chambers using LEDs and phototransistors. Assays are carried out on PDMS disposable microfluidic cartridges which require no external power for sample loading. We characterize the fluorescence detection limits, heater uniformity, and battery life of the instrument. As a proof-of-principle, we demonstrate the detection of the HIV-1 integrase gene with the µBAR using the Loop-Mediated Isothermal Amplification (LAMP) assay. Although we focus on the detection of purified DNA here, LAMP has previously been demonstrated with a range of clinical samples, and our eventual goal is to develop a microfluidic device which includes on-chip sample preparation from raw samples. The µBAR is based entirely around open source hardware and software, and in the accompanying online supplement we present a full set of schematics, bill of materials, PCB layouts, CAD drawings, and source code for the µBAR instrument with the goal of spurring further innovation toward low-cost genetic diagnostics.
Collapse
Affiliation(s)
- Frank B. Myers
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Berkeley Sensor and Actuator Center, University of California, Berkeley, California, United States of America
| | - Richard H. Henrikson
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Berkeley Sensor and Actuator Center, University of California, Berkeley, California, United States of America
| | - Jennifer Bone
- Department of Physics, University of California, Berkeley, California, United States of America
| | - Luke P. Lee
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Berkeley Sensor and Actuator Center, University of California, Berkeley, California, United States of America
- * E-mail:
| |
Collapse
|
20
|
Rapid visual detection of highly pathogenic Streptococcus suis serotype 2 isolates by use of loop-mediated isothermal amplification. J Clin Microbiol 2013; 51:3250-6. [PMID: 23884995 DOI: 10.1128/jcm.01183-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Streptococcus suis serotype 2 (S. suis 2) is an important zoonotic pathogen that causes considerable economic losses to the pig industry and significantly threatens public health worldwide. The highly pathogenic S. suis 2, which contains the 89K pathogenicity island (PAI), has caused large-scale outbreaks of infections in humans, resulting in high mortality rates. In this study, we established two loop-mediated isothermal amplification (LAMP)-based assays that can rapidly detect S. suis 2 and the 89K PAI and can be performed simultaneously under the same conditions. Further, based on the findings of these two LAMP assays and using the same set of serially diluted DNA samples, we compared the sensitivities of different LAMP product detection methods, including SYBR green detection, gel electrophoresis, turbidimetry, calcein assays, and hydroxynaphthol blue detection. The results suggest that target genes can be amplified and detected within 48 min under 63°C isothermal conditions. The sensitivity of tests for S. suis 2 detection varies between detection methods and reaction systems, indicating that for each LAMP reaction system, multiple detection methods should be performed to select the optimal one. The sensitivities of the optimized methods (7.16 copies/reaction) in the present study were identical to those of the real-time PCR assay, and the test results for reference strains and clinical samples showed that these LAMP systems have high specificities. Thus, since the LAMP systems established in this study are simple, fast, and sensitive, they may have good clinical potential for detecting the highly pathogenic S. suis 2.
Collapse
|
21
|
Zhao X, Chen X, Zhang Y, He X, Li W, Shi L, Chen X, Xu Z, Zhong N, Ji G, Yang L, Wang J. Development and evaluation of reverse-transcription loop-mediated isothermal amplification for rapid detection of human immunodeficiency virus type 1. Indian J Med Microbiol 2013. [PMID: 23183461 DOI: 10.4103/0255-0857.103757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE The objective of this study was to establish a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) method for rapid detection of human immunodeficiency virus type 1 (HIV-1). MATERIALS AND METHODS The HIV-1 integrase gene region was selected because it was a conserved part of the HIV-1 genome. Six primers specific to eight regions of the HIV-1 integrase gene were designed. A total of 171 samples (18 HIV-1 confirmed positive samples and 153 serum specimens were collected in this study) were tested by RT-LAMP and reverse-transcription polymerase chain reaction (RT-PCR). After amplification in an isothermal water bath for 45 min, samples containing HIV-1 generated the expected ladder-like products while other viruses generated no product. RESULTS The sensitivity and specificity of the RT-LAMP assay were evaluated by comparison with RT-PCR. The assay was significantly more sensitive than normal gel-based RT-PCR. CONCLUSION Because it is specific and simple, the RT-LAMP assay can be widely applied in clinical laboratories for rapid detection of HIV-1.
Collapse
Affiliation(s)
- Xihong Zhao
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073; College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Boyle DS, Lehman DA, Lillis L, Peterson D, Singhal M, Armes N, Parker M, Piepenburg O, Overbaugh J. Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification. mBio 2013; 4:e00135-13. [PMID: 23549916 PMCID: PMC3622927 DOI: 10.1128/mbio.00135-13] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 12/12/2022] Open
Abstract
Early diagnosis and treatment of human immunodeficiency virus type 1 (HIV-1) infection in infants can greatly reduce mortality rates. However, current infant HIV-1 diagnostics cannot reliably be performed at the point of care, often delaying treatment and compromising its efficacy. Recombinase polymerase amplification (RPA) is a novel technology that is ideal for an HIV-1 diagnostic, as it amplifies target DNA in <20 min at a constant temperature, without the need for complex thermocycling equipment. Here we tested 63 HIV-1-specific primer and probe combinations and identified two RPA assays that target distinct regions of the HIV-1 genome (long terminal repeat [LTR] and pol) and can reliably detect 3 copies of proviral DNA by the use of fluorescence detection and lateral-flow strip detection. These pol and LTR primers amplified 98.6% and 93%, respectively, of the diverse HIV-1 variants tested. This is the first example of an isothermal assay that consistently detects all of the major HIV-1 global subtypes.
Collapse
Affiliation(s)
- David S Boyle
- Program for Appropriate Technology in Health, Seattle, WA, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
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.
Collapse
Affiliation(s)
- Bing Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | | | | | | | | | | |
Collapse
|
24
|
Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid detection of enterovirus 71. BMC Infect Dis 2011; 11:197. [PMID: 21767352 PMCID: PMC3154872 DOI: 10.1186/1471-2334-11-197] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Accepted: 07/18/2011] [Indexed: 01/09/2023] Open
Abstract
Background Hand, foot, and mouth disease (HFMD) caused by enterovirus 71 (EV71) is very common in China. It is difficult to distinguish between EV71 and coxsackievirus A16 (CVA16) infections in clinical HFMD patients. Routine laboratory diagnosis of EV71 infection is time-consuming and requires expensive instruments. In this study, we have developed a one-step, single tube, reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for rapid and sensitive detection of EV71. Methods Six primers that can recognize 6 distinct regions on the VP2 gene of EV71 were designed for RT-LAMP assay. The amplification was completed by incubating all reagents in a single tube with reverse transcriptase and Bst DNA polymerase under the isothermal condition (60°C) for 60 min, and could be evaluated by using GoldView staining under a handheld ultraviolet torch lamp or electrophoresis analysis. Results A total of 123 specimens collected from suspicious patients with HFMD were simultaneously detected by RT-LAMP and PCR fluorescence probing assay. The RT-LAMP amplified products containing EV71 were digested by HinfI and TaqI restriction endonucleases; in contrast, non-specific products with CVA16, coxsackievirus A4 and coxsackievirus B3 could not be detected in RT-LAMP assay. Meanwhile, RT-LAMP assay could amplify EV71 virus with a detection limit of 1 PFU/ml within 60 min. Compared with PCR fluorescence probing assay, RT-LAMP assay exhibited 98.4% identity during the detection of EV71 viral RNA without the missing of positive samples. Conclusion Our results indicated that RT-LAMP is a rapid, sensitive, specific and accurate method for the detection of EV71 in clinical specimens. Therefore, this developed method has potential application for rapid and comprehensive surveillance for EV71 infection, especially in developing country.
Collapse
|