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Lai MY, Abdullah ML, Lau YL. Real-time fluorescence loop-mediated isothermal amplification assays for detection of zoonotic malaria Plasmodium parasites. Acta Trop 2024; 255:107249. [PMID: 38740319 DOI: 10.1016/j.actatropica.2024.107249] [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: 01/13/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Natural human infections by Plasmodium cynomolgi and P. inui have been reported recently and gain the substantial attention from Southeast Asian countries. Zoonotic transmission of non-human malaria parasites to humans from macaque monkeys occurred through the bites of the infected mosquitoes. The objective of this study is to establish real-time fluorescence loop-mediated isothermal amplification (LAMP) assays for the detection of zoonotic malaria parasites by combining real-time fluorescent technology with the isothermal amplification technique. METHODS By using 18S rRNA as the target gene, the primers for P. cynomolgi, P. coatneyi and P. inui were newly designed in the present study. Four novel real-time fluorescence LAMP assays were developed for the detection of P. cynomolgi, P. coatneyi, P. inui and P. knowlesi. The entire amplification process was completed in 60 min, with the assays performed at 65 °C. By using SYTO-9 as the nucleic acid intercalating dye, the reaction was monitored via real-time fluorescence signal. RESULTS There was no observed cross-reactivity among the primers from different species. All 70 field-collected monkey samples were successfully amplified by real-time fluorescence LAMP assays. The detection limit for P. cynomolgi, P. coatneyi and P. knowlesi was 5 × 109 copies/µL. Meanwhile, the detection limit of P. inui was 5 × 1010 copies/µL. CONCLUSION This is the first report of the detection of four zoonotic malaria parasites by real-time fluorescence LAMP approaches. It is an effective, rapid and simple-to-use technique. This presented platform exhibits considerable potential as an alternative detection for zoonotic malaria parasites.
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Affiliation(s)
- Meng Yee Lai
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Mohd Lutfi Abdullah
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division Department of Wildlife and National Parks Peninsular Malaysia, Jalan Cheras, 56100 Kuala Lumpur, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
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Nguyen HQ, Nguyen VD, Phan VM, Seo TS. Development of a self-contained microfluidic chip and an internet-of-things-based point-of-care device for automated identification of respiratory viruses. LAB ON A CHIP 2024; 24:2485-2496. [PMID: 38587207 DOI: 10.1039/d3lc00933e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The COVID-19 pandemic greatly impacted the in vitro diagnostic market, leading to the development of new technologies such as point-of-care testing (POCT), multiplex testing, and digital health platforms. In this study, we present a self-contained microfluidic chip integrated with an internet-of-things (IoT)-based point-of-care (POC) device for rapid and sensitive diagnosis of respiratory viruses. Our platform enables sample-to-answer diagnostics within 70 min by automating RNA extraction, reverse transcription-loop-mediated isothermal amplification (RT-LAMP), and fluorescence detection. The microfluidic chip is designed to store all the necessary reagents for the entire diagnostic assay, including a lysis buffer, a washing buffer, an elution buffer, and a lyophilized RT-LAMP cocktail. It can perform nucleic acid extraction, aliquoting, and gene amplification in multiple reaction chambers without cross-contamination. The IoT-based POC device consists of a Raspberry Pi 4 for device control and data processing, a CMOS sensor for measuring fluorescence signals, a resistive heater panel for temperature control, and solenoid valves for controlling the movement of on-chip reagent solutions. The proposed device is portable and features a touchscreen for user control and result display. We evaluated the performance of the platform using 11 clinical respiratory virus samples, including 5 SARS-CoV-2 samples, 2 influenza A samples, and 4 influenza B samples. All tested clinical samples were accurately identified with high specificity and fidelity, demonstrating the ability to simultaneously detect multiple respiratory viruses. The combination of the integrated microfluidic chip with the POC device offers a simple, cost-effective, and scalable solution for rapid molecular diagnosis of respiratory viruses in resource-limited settings.
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Affiliation(s)
- Huynh Quoc Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin, 17104, South Korea.
| | - Van Dan Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin, 17104, South Korea.
| | - Vu Minh Phan
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin, 17104, South Korea.
| | - Tae Seok Seo
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin, 17104, South Korea.
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3
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Ma L, Zhu H, Jiang Y, Kong X, Gao P, Liu Y, Zhao M, Deng G, Cao Y. Development of a Novel Multiplex PCR Method for the Rapid Detection of SARS-CoV-2, Influenza A Virus, and Influenza B Virus. Int J Anal Chem 2024; 2024:4950391. [PMID: 38456096 PMCID: PMC10919977 DOI: 10.1155/2024/4950391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/03/2024] [Accepted: 02/10/2024] [Indexed: 03/09/2024] Open
Abstract
Objective A sensitive and specific multiplex fluorescence rapid detection method was established for simultaneous detection of SARS-CoV-2, influenza A virus, and influenza B virus in a self-made device within 30 min, with a minimum detection limit of 200 copies/mL. Methods Based on the genome sequences of SARS-CoV-2, influenza A virus (FluA), and influenza B virus (FluB) with reference to the Chinese Center for Disease Control and Prevention and related literature, specific primers were designed, and a multiplex fluorescent PCR system was established. The simultaneous and rapid detection of SARS-CoV-2, FluA, and FluB was achieved by optimizing the concentrations of Taq DNA polymerase as well as primers, probes, and Mg2+. The minimum detection limits of the nucleic acid rapid detection system for SARS-CoV-2, FluA, and FluB were evaluated. Results By optimizing the amplification system, the N enzyme with the best amplification performance was selected, and the optimal concentration of Mg2+ in the multiamplification system was 3 mmol/L; the final concentrations of SARS-CoV-2 NP probe and primer were 0.15 μmol/L and 0.2 μmol/L, respectively; the final concentrations of SARS-CoV-2 ORF probe and primer were both 0.15 μmol/L; the final concentrations of FluA probe and primer were 0.2 μmol/L and 0.3 μmol/L, respectively; the final concentrations of FluB probe and primer were 0.15 μmol/L and 0.25 μmol/L, respectively. Conclusion A multiplex real-time quantitative fluorescence RT-PCR system for three respiratory viruses of SARS-CoV-2, FluA, and FluB was established with a high amplification efficiency and sensitivity reaching 200 copies/mL for all samples. Combined with the automated microfluidic nucleic acid detection system, the system can achieve rapid detection in 30 minutes.
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Affiliation(s)
- Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Haoyan Zhu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Guoxiong Deng
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, China
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Rapid and precise detection of cryptic tea pathogen Exobasidium vexans: RealAmp validation of LAMP approach. World J Microbiol Biotechnol 2022; 39:52. [PMID: 36564678 DOI: 10.1007/s11274-022-03506-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
This work embodies the development of a real time loop mediated isothermal amplification (RealAmp) assay for the rapid detection of the cryptic tea phytopathogen, Exobasidium vexans, the causal organism of blister blight disease. Due to the widespread popularity of tea as a beverage and the associated agro-economy, the rapid detection and management of the fast-spreading blister blight disease have been a longstanding necessity. Loop-mediated isothermal amplification (LAMP) primers were designed targeting the E. vexans ITS rDNA region and the reaction temperature was optimized at 62 °C with a 60 min reaction time. Amplification of the E. vexans isolates in the initial LAMP reactions was confirmed by both agarose gel electrophoresis and SYBR Green I dye based colour change visualization. The specificity of the LAMP primers for E. vexans was validated by negative testing of seven different phytopathogenic test fungi using LAMP and RealAmp assay. The positive findings in RealAmp assay for E. vexans strain were corroborated via detecting fluorescence signals in real-time. Further, the LAMP assays performed with gDNA isolated from infected tea leaves revealed positive amplification for the presence of E. vexans. The results demonstrate that this rapid and precise RealAmp assay has the potential to be applied for field-based detection of E. vexans in real-time.
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Owoicho O, Olwal CO, Tettevi EJ, Atu BO, Durugbo EU. Loop-mediated isothermal amplification for Candida species surveillance in under-resourced setting: a review of evidence. Expert Rev Mol Diagn 2022; 22:643-653. [PMID: 35920288 DOI: 10.1080/14737159.2022.2109963] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Non-albicans Candida species (NACS) have emerged as a major public health burden although they are still underappreciated. Some NACS have intrinsic antifungal resistance, requiring constant surveillance to improve patient care and thwart outbreaks of recalcitrant candida infections. However, effective Candida species surveillance has relied on PCR-based or other high-end techniques that are largely unaffordable in under-resourced countries. Loop-mediated isothermal amplification (LAMP) has emerged as a potentially effective and affordable technique for infectious disease surveillance, especially in under resourced settings. AREAS COVERED We critically reviewed current literature on application of LAMP for Candida species identification in pure fungal isolates, and in clinical and non-clinical samples. EXPERT OPINION LAMP has been studied for Candida species identification, including the NACS. Besides a short turnaround time, LAMP has analytical sensitivity and specificity that are not only higher than culture method but also comparable with conventional and quantitative PCR techniques. However, extensive evaluation of LAMP for Candida species detection using various types of clinical and environmental samples are required before deploying the technique for Candida species surveillance.
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Affiliation(s)
- Oloche Owoicho
- Department of Biological Sciences, Benue State University, P.M.B. 102119, Makurdi, Benue State, Nigeria
| | | | - Edward Jenner Tettevi
- Biomedical and Public Health Research Unit, Water Research Institute, Council for Scientific and Industrial Research, Accra, Ghana
| | - Bernard Ortwer Atu
- Department of Biological Sciences, Benue State University, P.M.B. 102119, Makurdi, Benue State, Nigeria
| | - Ernest Uzodimma Durugbo
- Department of Biological Sciences, Redeemer's University, P.M.B. 230, Ede, Osun State, Nigeria
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Baker AN, Hawker-Bond GW, Georgiou PG, Dedola S, Field RA, Gibson MI. Glycosylated gold nanoparticles in point of care diagnostics: from aggregation to lateral flow. Chem Soc Rev 2022; 51:7238-7259. [PMID: 35894819 PMCID: PMC9377422 DOI: 10.1039/d2cs00267a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Current point-of-care lateral flow immunoassays, such as the home pregnancy test, rely on proteins as detection units (e.g. antibodies) to sense for analytes. Glycans play a fundamental role in biological signalling and recognition events such as pathogen adhesion and hence they are promising future alternatives to antibody-based biosensing and diagnostics. Here we introduce the potential of glycans coupled to gold nanoparticles as recognition agents for lateral flow diagnostics. We first introduce the concept of lateral flow, including a case study of lateral flow use in the field compared to other diagnostic tools. We then introduce glycosylated materials, the affinity gains achieved by the cluster glycoside effect and the current use of these in aggregation based assays. Finally, the potential role of glycans in lateral flow are explained, and examples of their successful use given. Antibody-based lateral flow (immune) assays are well established, but here the emerging concept and potential of using glycans as the detection agents is reviewed.![]()
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Affiliation(s)
- Alexander N Baker
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK.
| | - George W Hawker-Bond
- Oxford University Clinical Academic Graduate School, John Radcliffe Hospital Oxford, Oxford, OX3 9DU, UK
| | - Panagiotis G Georgiou
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK.
| | | | - Robert A Field
- Iceni Glycoscience Ltd, Norwich, NR4 7GJ, UK.,Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK. .,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, CV4 7AL, Coventry, UK
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Jhou YR, Wang CH, Tsai HP, Shan YS, Lee GB. An integrated microfluidic platform featuring real-time reverse transcription loop-mediated isothermal amplification for detection of COVID-19. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 358:131447. [PMID: 35095200 PMCID: PMC8789398 DOI: 10.1016/j.snb.2022.131447] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 05/12/2023]
Abstract
An integrated microfluidic platform (IMP) utilizing real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) was developed here for detection and quantification of three genes of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; i.e., coronavirus diseases 2019 (COVID-19)): RNA-dependent RNA polymerase, the envelope gene, and the nucleocapsid gene for molecular diagnosis. The IMP comprised a microfluidic chip, a temperature control module, a fluidic control module that collectively carried out viral lysis, RNA extraction, RT-LAMP, and the real-time detection within 90 min in an automatic format. A limit of detection of 5 × 103 copies/reaction for each gene was determined with three samples including synthesized RNAs, inactive viruses, and RNAs extracted from clinical samples; this compact platform could be a useful tool for COVID-19 diagnostics.
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Affiliation(s)
- You-Ru Jhou
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
- Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Nano Engineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
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Jhou YR, Wang CH, Tsai HP, Shan YS, Lee GB. An integrated microfluidic platform featuring real-time reverse transcription loop-mediated isothermal amplification for detection of COVID-19. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 358:131447. [PMID: 35095200 DOI: 10.1016/j.snb.2022.131497] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 05/24/2023]
Abstract
An integrated microfluidic platform (IMP) utilizing real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) was developed here for detection and quantification of three genes of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; i.e., coronavirus diseases 2019 (COVID-19)): RNA-dependent RNA polymerase, the envelope gene, and the nucleocapsid gene for molecular diagnosis. The IMP comprised a microfluidic chip, a temperature control module, a fluidic control module that collectively carried out viral lysis, RNA extraction, RT-LAMP, and the real-time detection within 90 min in an automatic format. A limit of detection of 5 × 103 copies/reaction for each gene was determined with three samples including synthesized RNAs, inactive viruses, and RNAs extracted from clinical samples; this compact platform could be a useful tool for COVID-19 diagnostics.
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Affiliation(s)
- You-Ru Jhou
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
- Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Nano Engineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
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Gomez-Gutierrez SV, Goodwin SB. Loop-Mediated Isothermal Amplification for Detection of Plant Pathogens in Wheat ( Triticum aestivum). FRONTIERS IN PLANT SCIENCE 2022; 13:857673. [PMID: 35371152 PMCID: PMC8965322 DOI: 10.3389/fpls.2022.857673] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/17/2022] [Indexed: 05/31/2023]
Abstract
Wheat plants can be infected by a variety of pathogen species, with some of them causing similar symptoms. For example, Zymoseptoria tritici and Parastagonospora nodorum often occur together and form the Septoria leaf blotch complex. Accurate detection of wheat pathogens is essential in applying the most appropriate disease management strategy. Loop-mediated isothermal amplification (LAMP) is a recent molecular technique that was rapidly adopted for detection of plant pathogens and can be implemented easily for detection in field conditions. The specificity, sensitivity, and facility to conduct the reaction at a constant temperature are the main advantages of LAMP over immunological and alternative nucleic acid-based methods. In plant pathogen detection studies, LAMP was able to differentiate related fungal species and non-target strains of virulent species with lower detection limits than those obtained with PCR. In this review, we explain the amplification process and elements of the LAMP reaction, and the variety of techniques for visualization of the amplified products, along with their advantages and disadvantages compared with alternative isothermal approaches. Then, a compilation of analyses that show the application of LAMP for detection of fungal pathogens and viruses in wheat is presented. We also describe the modifications included in real-time and multiplex LAMP that reduce common errors from post-amplification detection in traditional LAMP assays and allow discrimination of targets in multi-sample analyses. Finally, we discuss the utility of LAMP for detection of pathogens in wheat, its limitations, and current challenges of this technique. We provide prospects for application of real-time LAMP and multiplex LAMP in the field, using portable devices that measure fluorescence and turbidity, or facilitate colorimetric detection. New technologies for detection of plant pathogen are discussed that can be integrated with LAMP to obtain elevated analytical sensitivity of detection.
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Hajeri S, Yokomi R. Immunocapture-Reverse Transcriptase Loop-Mediated Isothermal Amplification Assay for Detection of Plant RNA Viruses. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2400:245-252. [PMID: 34905207 DOI: 10.1007/978-1-0716-1835-6_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a sensitive method that can rapidly amplify a specific nucleic acid target with high specificity. The LAMP reaction process has no denaturation step, instead DNA amplification occurs by strand displacement activity of the Bacillus stearothermophilus (Bst) DNA polymerase under isothermal conditions. It utilizes three sets of forward and reverse oligonucleotide primers specific to six distinct sequences on the target gene. These primers are used to generate amplification products that contain single-stranded loops, thereby allowing primers to bind to these sequences without the need for repeated cycles of thermal denaturation. For diagnosis of pathogens with RNA genome, LAMP has been merged with reverse transcription (RT) step to create RT-LAMP. To further reduce the cost of diagnosis and increase the throughput, immunocapture (IC) step was added to develop IC-RT-LAMP assay. Hence, this chapter focuses on utilizing IC-RT-LAMP assay to specifically identify severe strain of a plant virus from field samples.
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Affiliation(s)
- Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA, USA.
| | - Raymond Yokomi
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
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Ghosh S, Straus DL, Good C, Phuntumart V. Development and comparison of loop-mediated isothermal amplification with quantitative PCR for the specific detection of Saprolegnia spp. PLoS One 2021; 16:e0250808. [PMID: 34898622 PMCID: PMC8668100 DOI: 10.1371/journal.pone.0250808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 11/07/2021] [Indexed: 11/26/2022] Open
Abstract
Saprolegniasis is an important disease in freshwater aquaculture, and is associated with oomycete pathogens in the genus Saprolegnia. Early detection of significant levels of Saprolegnia spp. pathogens would allow informed decisions for treatment which could significantly reduce losses. This study is the first to report the development of loop-mediated isothermal amplification (LAMP) for the detection of Saprolegnia spp. and compares it with quantitative PCR (qPCR). The developed protocols targeted the internal transcribed spacer (ITS) region of ribosomal DNA and the cytochrome C oxidase subunit 1 (CoxI) gene and was shown to be specific only to Saprolegnia genus. This LAMP method can detect as low as 10 fg of S. salmonis DNA while the qPCR method has a detection limit of 2 pg of S. salmonis DNA, indicating the superior sensitivity of LAMP compared to qPCR. When applied to detect the pathogen in water samples, both methods could detect the pathogen when only one zoospore of Saprolegnia was present. We propose LAMP as a quick (about 20–60 minutes) and sensitive molecular diagnostic tool for the detection of Saprolegnia spp. suitable for on-site applications.
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Affiliation(s)
- Satyaki Ghosh
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - David L. Straus
- United States Department of Agriculture, Agricultural Research Service, Harry K. Dupree-Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas, United States of America
| | - Christopher Good
- The Conservation Fund’s Freshwater Institute, Shepherdstown, West Virginia, United States of America
| | - Vipaporn Phuntumart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
- * E-mail:
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Xiao C, Li R. Detection and Control of Fusarium oxysporum from Soft Rot in Dendrobium officinale by Loop-Mediated Isothermal Amplification Assays. BIOLOGY 2021; 10:1136. [PMID: 34827129 PMCID: PMC8615024 DOI: 10.3390/biology10111136] [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] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/15/2023]
Abstract
Soft rot causing Fusarium oxysporum is one of the most destructive diseases of Dendrobium officinale Kimura et Migo in China that reduces D. officinale yield and quality. A key challenge for an integrated management strategy for this disease is the rapid and accurate detection of F. oxysporum on D. officinale. Therefore, a new loop-mediated isothermal amplification (LAMP) assay was developed for this purpose. In this study, the primers were selected and designed using the translation elongation factor-1α (TEF-1α) gene region as the target DNA sequence in order to screen the best system of reaction of LAMP to detect F. oxysporum through optimizing different conditions of the LAMP reaction, including time, temperature, concentrations of MgSO4, and concentrations of inner and outer primers. The optimized system was able to efficiently amplify the target gene at 62 °C for 60 min with 1.2 μM internal primers, 0.4 μM external primers, 7 mM Mg2+, and 5 fg/µL minimum detection concentration of DNA for F. oxysporum. The amplified products could be detected with the naked eye after completion of the reaction with SYBR green I. We were better able to control the effect of soft rot in D. officinale using fungicides following a positive test result. Additionally, the control effect of synergism combinations against soft rot was higher than 75%. Thus, LAMP assays could detect F. oxysporum in infected tissues of D. officinale and soils in field, allowing for early diagnosis of the disease.
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Affiliation(s)
- Caiyun Xiao
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China;
- The Provincial Key Laboratory for Agricultural Pest Management in Mountainous Region, Guiyang 550025, China
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Rongyu Li
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China;
- The Provincial Key Laboratory for Agricultural Pest Management in Mountainous Region, Guiyang 550025, China
- College of Agriculture, Guizhou University, Guiyang 550025, China
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Nguyen HA, Lee NY. Polydopamine aggregation: A novel strategy for power-free readout of loop-mediated isothermal amplification integrated into a paper device for multiplex pathogens detection. Biosens Bioelectron 2021; 189:113353. [PMID: 34049080 DOI: 10.1016/j.bios.2021.113353] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/23/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) has been widely used for detecting pathogens. However, power-free and clear visualization of results still remain challenging. In this study, we developed a paper device integrated with power-free DNA detection strategy realized by polydopamine aggregation. In the presence of DNA amplicons, the polymerization of dopamine into aggregated polydopamine was hindered, while in the absence of DNA amplicons, polydopamine aggregation is facilitated. The porosity of the paper enabled the capillary flow of dispersed polydopamine for positive sample, while aggregated polydopamine remained at the bottom of the paper strip due to large size of the aggregates for negative sample. Based on this mechanism, we fabricated a slidable paper device integrating LAMP with dopamine polymerization for the naked-eye detection, operated in a seamless manner. Moreover, the introduced paper device was successfully used to detect DNA extracted from Escherichia coli O157:H7 and SARS-CoV-2 within 25 min, as well as Enterococcus faecium within 35 min. The detection limits of both Escherichia coli O157:H7 and SARS-CoV-2 were 10-4 ng/μL. The introduced paper device can be used as a simple and sensitive tool for detecting multiple infectious pathogens, making it an ideal tool particularly for resource-limited environment.
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Affiliation(s)
- Hanh An Nguyen
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea.
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14
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Zhang J, Wang L, Shi L, Chen X, Liang M, Zhao L. Development and application of a real-time loop-mediated isothermal amplification method for quantification of Acetobacter aceti in red wine. FEMS Microbiol Lett 2020; 367:5918383. [PMID: 33021644 DOI: 10.1093/femsle/fnaa152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/03/2020] [Indexed: 01/01/2023] Open
Abstract
This study reports the development and optimization of a real-time loop-mediated isothermal amplification (qLAMP) method for rapid detection of Acetobacter aceti strain in red wine samples. Our results showed that the primers and probes designed for 16S rRNA were effective for A. aceti detection. The quantification limit of real-time polymerase chain reaction (qPCR) and qLAMP in pure culture was 2.05 × 101 colony forming units (CFU) mL-1. qLAMP had a sensitivity of 6.88 × 101 CFU mL-1 in artificially contaminated Changyu dry red wine (CDRW) and Changyu red wine (CRW), and 6.88 × 102 CFU mL-1 in artificially contaminated Greatwall dry red wine (GDRW), which was 10 times higher than that of qPCR. In conclusion, this newly developed qLAMP is a reliable, rapid and accurate method for the detection and quantification of A. aceti species in red wine samples. Furthermore, our work provides a standard reference method for the quantitative detection of A. aceti and other acetic acid bacteria during the fermentation and storage of red wine samples.
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Affiliation(s)
- Jingfeng Zhang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Li Wang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, 510642, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, 510632, China
| | - Xun Chen
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, 510632, China
| | - Meidan Liang
- Guagnzhou Institute for Food Inspection, Guangzhou, 510006, China
| | - Lichao Zhao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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15
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Loop Mediated Isothermal Amplification: A Promising Tool for Screening Genetic Mutations. Mol Diagn Ther 2020; 23:723-733. [PMID: 31396882 DOI: 10.1007/s40291-019-00422-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutation screening is elemental for clinical diagnosis and in determining therapeutic strategies. Nucleic acid-based techniques are considered to be the most accurate tools in genetic diagnosis. One such technique is loop-mediated isothermal amplification (LAMP) assay, which has seen tremendous applications in recent years. The advantages of the assay lie in its rapidity, efficiency, sensitivity, and cost. It works in isothermal conditions and amplifies the target gene using DNA polymerases that have strand displacement activity. To date, the assay has been widely used in different fields of research, including pathogen detection, crop development, and disease diagnosis. However, despite the potential, its application in mutation screening has been minimal. This review highlights the LAMP assay and its variants that have been developed for screening single-nucleotide polymorphisms and gene translocations in cancer.
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16
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Li HW, Mao JY, Lien CW, Wang CK, Lai JY, Mandal RP, Chang HT, Chang L, Ma DHK, Huang CC. Platinum ions mediate the interactions between DNA and carbon quantum dots: diagnosis of MRSA infections. J Mater Chem B 2020; 8:3506-3512. [PMID: 31859331 DOI: 10.1039/c9tb02468a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we have developed a rapid and cost-effective method employing platinum ion (Pt4+)-capped fluorescent carbon quantum dots (CQDs) coupled with loop-mediated isothermal amplification (LAMP) to detect dual MRSA genes. We synthesized nitrogen- and chlorine-co-doped fluorescent CQDs (CQDSPDs) from spermidine trihydrochloride via a simple one-step pyrolysis. The CQDSPDs capped with Pt4+ ions through the cooperative coordination of the amine and chlorine groups on the surface of CQDs facilitated the double-stranded DNA (dsDNA)-induced fluorescence quenching of CQDs, and enabled the construction of the CQDSPDs/Pt4+ probe for the detection of as few as 10 copies of the MRSA gene (mecA and femA). The sensitivity and specificity of the CQDSPDs/Pt4+ probe for MRSA detection in clinical specimens (n = 24) were 94% and 86%, respectively. Our results reveal that the CQDSPDs/Pt4+ probe has great potential for the diagnosis of antibiotic-resistant superbugs with high sensitivity, specificity, and agreement.
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Affiliation(s)
- Han-Wei Li
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan.
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17
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Selvaraj V, Maheshwari Y, Hajeri S, Yokomi R. A rapid detection tool for VT isolates of Citrus tristeza virus by immunocapture-reverse transcriptase loop-mediated isothermal amplification assay. PLoS One 2019; 14:e0222170. [PMID: 31487325 PMCID: PMC6728045 DOI: 10.1371/journal.pone.0222170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 08/21/2019] [Indexed: 11/18/2022] Open
Abstract
Severe strains of Citrus tristeza virus (CTV) cause quick decline and stem pitting resulting in significant economic losses in citrus production. A immunocapture reverse-transcriptase loop-mediated amplification (IC-RT-LAMP) assay was developed in this study to detect the severe VT strains that are typically associated with severe CTV symptoms. The sensitivity of RT-LAMP assay was determined by ten-fold serial dilutions of CA-VT-AT39 RNA, in comparison to one-step RT-droplet digital (dd) PCR. RT-LAMP detected up to 0.002 ng RNA with an amplification time of 10:35 (min:sec.), equivalent to 11.3 copies as determined by one step RT-ddPCR. The RT-LAMP assay specifically detected CA-VT-AT39 RNA and did not cross react with other CTV genotypes tested (T36, T30, RB, S1 and T68). To facilitate rapid on-site detection, the RT-LAMP assay was improved by first capturing the CTV virions from citrus crude leaf sap using CTV-IgG (IC-RT-LAMP), thereby eliminating nucleic acid extraction steps. IC-RT-LAMP assay was optimized with two-fold dilutions of CTV-IgG ranging from 1:500 to 1:16,000. The IC-RT-LAMP assay detected the CA-VT-AT39 virions in all dilutions tested. The minimum amplification time was 6:45 (min:sec) with 1:500 and 1:1000 of CTV-IgG dilutions. The limit of detection of IC-RT-LAMP assay with crude leaf sap of CA-VT-AT39 was 1:320 with a maximum amplification time of 9:08 (min:sec). The IC-RT-LAMP assay was validated for VT genotype by comparing to IC-RT-qPCR using the CTV from 40 field tree samples. A 100% agreement was observed between tests, regardless of single or mixed infections of CTV VT with other genotypes. Therefore, the IC-RT-LAMP assay can serve as a useful tool in the management of potentially severe strains of CTV.
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Affiliation(s)
- Vijayanandraj Selvaraj
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
| | - Yogita Maheshwari
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA, United States of America
| | - Raymond Yokomi
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
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18
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Cao W, Li Y, Chen X, Chang Y, Li L, Shi L, Bai W, Ye L. Species identification and quantification of silver pomfret using the droplet digital PCR assay. Food Chem 2019; 302:125331. [PMID: 31404867 DOI: 10.1016/j.foodchem.2019.125331] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/30/2019] [Accepted: 08/04/2019] [Indexed: 11/30/2022]
Abstract
Adulteration of the high-value silver pomfret (Pampus argenteus) is a serious problem worldwide, necessitating accurate identification and quantification of the species. In this study, optimisation of the digital droplet PCR (ddPCR) assay for the identification and quantification of the silver pomfret was carried out. The primer and probe concentrations, melting temperature, and PCR cycle number were optimised by combining single-factor experiments with an orthogonal experimental design. The absolute limits of detection and quantification of the ddPCR were 2copies/μl and 21 copies/μl, respectively. Its sensitivity was 0.1% for meat mixtures and 0.5% for DNA mixtures. The ddPCR was 156 times more sensitive than the real-time PCR, although both methods had similar specificities. However, the overall time needed to complete the ddPCR method was twice that of the real-time PCR. Notwithstanding, the ddPCR methodology established in this study can be a valuable tool for addressing species adulteration issues.
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Affiliation(s)
- Weiwei Cao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yiming Li
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510641, Guangdong, China
| | - Xun Chen
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yanlei Chang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Weibin Bai
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Lei Ye
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China.
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