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Saifuddin SA, Rashid R, Nor Azmi NJ, Mohamad S. Colorimetric strategies applicable for loop-mediated isothermal amplification. J Microbiol Methods 2024; 223:106981. [PMID: 38945305 DOI: 10.1016/j.mimet.2024.106981] [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: 02/22/2023] [Revised: 05/20/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
In recent years, loop-mediated isothermal amplification (LAMP) has gained popularity for detecting various pathogen-specific genes due to its superior sensitivity and specificity compared to conventional polymerase chain reaction (PCR). The simplicity and flexibility of naked-eye detection of the amplicon make LAMP an ideal rapid and straightforward diagnostic tool, especially in resource-limited laboratories. Colorimetric detection is one of the simplest and most straightforward among all detection methods. This review will explore various colorimetric dyes used in LAMP techniques, examining their reaction mechanisms, advantages, limitations and latest applications.
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Affiliation(s)
- Syaidatul Akmal Saifuddin
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Roslina Rashid
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Nurin Jazlina Nor Azmi
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Suharni Mohamad
- School of Dental Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.
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2
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Lakshminarayana Reddy CN, Venkataravanappa V, Chowdappa A, Shridhar H, Mantesh M, Vinaykumar HD, Krishna Reddy M. Complete genome characterization of chilli veinal mottle virus associated with mosaic and mottling disease of tomato and development of LAMP assay for quick detection. 3 Biotech 2024; 14:139. [PMID: 38682094 PMCID: PMC11052978 DOI: 10.1007/s13205-024-03984-x] [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: 07/31/2023] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Chilli veinal mottle virus (ChiVMV) is a potyvirus known to cause havoc in many solanaceous crops. Samples from tomato plants exhibiting typical mosaic and mottling symptoms in two locations from farmers' fields were collected and tested using DAC ELISA for the presence of ChiVMV and other viruses known to infect tomato. ChiVMV Gauribidanur isolate from infected tomato was mechanically inoculated to Datura metel, Nicotiana tabacum, Nicotiana benthamiana, Nicotiana glutinosa, chilli, and tomato plants which exhibited systemic mosaic and mottling symptoms 10 days post-inoculation. This results were further confirmed by RT-PCR and DAC ELISA using CP gene-specific primers and ChiVMV antisera, respectively. Transmission electron microscopy revealed the presence of long filamentous particles (800 × 11 nm) resembling viruses in the Potyviridae family. The complete genome of ChiVMV comprised 9716 nucleotides except for poly A tail, with a predicted open reading frame spanning 9270 nucleotides encoding polyproteins of 3089 amino acids. Comparative analysis revealed that ChiVMV-tomato isolates reported across the world shared maximum nucleotide identity (93-96.7%) with chilli isolates from India and Pakistan. These results were well supported by sequence demarcation analysis. Further, the Neibhor-Net network analysis of the complete genome of ChiVMV-tomato, along with other host isolates, formed a reticular network phylogenetic tree suggesting recombination events. Subsequently, RDP5 detected intra-specific recombination breakpoints at the positions 1656-5666 nucleotides with major parent ChiVMV (MN508960) Uravakonda and minor parent ChiVMV (MN508956) with a significant average p value of 1.905 × 10-22. The LAMP assay using ChiVMV-specific primers resulted in ladder-like amplified products on electrophoresed gel and a distinct red colour pattern with hydroxy naphthalene blue, indicating a positive reaction for the presence of ChiVMV in infected tomato samples. To validate LAMP-designed primers, RNA extracted from ChiVMV-infected tomato, chilli, datura, and tobacco samples were subjected to LAMP assay and it accurately detected the presence of ChiVMV in infected plant samples. Overall, this study provides holistic information of ChiVMV infecting tomato, spanning diagnosis, transmission, genetic characterization, and detection of recombination events, which collectively contribute to effective disease management, crop protection, and informed decision-making in agricultural practices.
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Affiliation(s)
- C. N. Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bangalore, Karnataka 560065 India
| | - V. Venkataravanappa
- Division of Plant Pathology, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
| | - A. Chowdappa
- Division of Plant Pathology, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
| | - H. Shridhar
- CSIR- North East Institute of Science and Technology, Jorhat, Assam 785006 India
| | - M. Mantesh
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bangalore, Karnataka 560065 India
| | - H. D. Vinaykumar
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bangalore, Karnataka 560065 India
| | - M. Krishna Reddy
- Division of Plant Pathology, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
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3
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Development of an on-spot and rapid recombinase polymerase amplification assay for Aspergillus flavus detection in grains. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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4
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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Waliullah S, Ling KS, Cieniewicz EJ, Oliver JE, Ji P, Ali ME. Development of Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Cucurbit Leaf Crumple Virus. Int J Mol Sci 2020; 21:ijms21051756. [PMID: 32143404 PMCID: PMC7084362 DOI: 10.3390/ijms21051756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/16/2022] Open
Abstract
A loop-mediated isothermal amplification (LAMP) assay was developed for simple, rapid and efficient detection of Cucurbit leaf crumple virus (CuLCrV), one of the most important begomoviruses that infects cucurbits worldwide. A set of six specific primers targeting a total 240 nt sequence regions in the DNA A of CuLCrV were designed and synthesized for detection of CuLCrV from infected leaf tissues using real-time LAMP amplification with the Genie® III system, which was further confirmed by gel electrophoresis and SYBR™ Green I DNA staining for visual observation. The optimum reaction temperature and time were determined, and no cross-reactivity was seen with other begomoviruses. The LAMP assay could amplify CuLCrV from a mixed virus assay. The sensitivity assay demonstrated that the LAMP reaction was more sensitive than conventional PCR, but less sensitive than qPCR. However, it was simpler and faster than the other assays evaluated. The LAMP assay also amplified CuLCrV-infected symptomatic and asymptomatic samples more efficiently than PCR. Successful LAMP amplification was observed in mixed virus-infected field samples. This simple, rapid, and sensitive method has the capacity to detect CuLCrV in samples collected in the field and is therefore suitable for early detection of the disease to reduce the risk of epidemics.
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Affiliation(s)
- Sumyya Waliullah
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.W.); (J.E.O.); (P.J.)
| | - Kai-Shu Ling
- U. S. Vegetable Laboratory, USDA-ARS, Charleston, SC 29414, USA;
| | | | - Jonathan E. Oliver
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.W.); (J.E.O.); (P.J.)
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.W.); (J.E.O.); (P.J.)
| | - Md Emran Ali
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.W.); (J.E.O.); (P.J.)
- Correspondence:
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Zhao VXT, Wong TI, Zheng XT, Tan YN, Zhou X. Colorimetric biosensors for point-of-care virus detections. MATERIALS SCIENCE FOR ENERGY TECHNOLOGIES 2020; 3:237-249. [PMID: 33604529 PMCID: PMC7148662 DOI: 10.1016/j.mset.2019.10.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 05/05/2023]
Abstract
Colorimetric biosensors can be used to detect a particular analyte through color changes easily by naked eyes or simple portable optical detectors for quantitative measurement. Thus, it is highly attractive for point-of-care detections of harmful viruses to prevent potential pandemic outbreak, as antiviral medication must be administered in a timely fashion. This review paper summaries existing and emerging techniques that can be employed to detect viruses through colorimetric assay design with detailed discussion of their sensing principles, performances as well as pros and cons, with an aim to provide guideline on the selection of suitable colorimetric biosensors for detecting different species of viruses. Among the colorimetric methods for virus detections, loop-mediated isothermal amplification (LAMP) method is more favourable for its faster detection, high efficiency, cheaper cost, and more reliable with high reproducible assay results. Nanoparticle-based colorimetric biosensors, on the other hand, are most suitable to be fabricated into lateral flow or lab-on-a-chip devices, and can be coupled with LAMP or portable PCR systems for highly sensitive on-site detection of viruses, which is very critical for early diagnosis of virus infections and to prevent outbreak in a swift and controlled manner.
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Affiliation(s)
- Victoria Xin Ting Zhao
- College of Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Ten It Wong
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Xin Ting Zheng
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Yen Nee Tan
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
- Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
| | - Xiaodong Zhou
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
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Zhang M, Ye J, He JS, Zhang F, Ping J, Qian C, Wu J. Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review. Anal Chim Acta 2019; 1099:1-15. [PMID: 31986265 DOI: 10.1016/j.aca.2019.11.056] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/15/2022]
Abstract
Nucleic acid-based techniques could achieve highly sensitive detection by amplifying template molecules to millions of folds. It has been one of the most valued analytical methods and is applied in many detection fields, such as diagnosis of infectious diseases, food safety assurance and so on. Nucleic acid-based techniques consist of three steps: nucleic acid extraction, amplification, and product detection. Among them, the detection step plays a vital role because it shows the results directly. As the trend of detection is simple, rapid and instrument-free, it is of necessity to carry out visual detection, where the result read-out could be visible and distinguished by the naked eye. In this critical review, advanced visual detection methods are summarized and discussed in detail, aiming to promote the potential application in on-site detection.
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Affiliation(s)
- Mengyao Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jing Ye
- Zhijiangnan Think Tank, Zhejiang Institute of Science and Technology Information, Hangzhou, 310006, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China.
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Development of a simple and rapid reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay for sensitive detection of Citrus tristeza virus. J Virol Methods 2017; 250:6-10. [DOI: 10.1016/j.jviromet.2017.09.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/21/2017] [Accepted: 09/05/2017] [Indexed: 11/18/2022]
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9
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Lu Y, Yao B, Wang G, Hong N. The detection of ACLSV and ASPV in pear plants by RT-LAMP assays. J Virol Methods 2017; 252:80-85. [PMID: 29180245 DOI: 10.1016/j.jviromet.2017.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of Apple chlorotic leaf spot virus (ACLSV) and Apple stem pitting virus (ASPV), two important viruses frequently occurring in pear trees. A set of four RT-LAMP primers designed based on the highly conserved region of each CP gene of the two viruses showed high specificity and feasibility for ACLSV and ASPV detections. The RT-LAMP assays for ACLSV and ASPV in pear samples were 104 and 103 times more sensitive than that of conventional RT-PCR assays. The RT-LAMP under optimal reaction condition was subsequently utilized in the detection of the two viruses in-vitro cultures of pear and field pear samples. This study provides a rapid and sensitive tool to determine the infection statues of the two viruses in pear certification program.
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Affiliation(s)
- Yongcan Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bingyu Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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Panferov VG, Safenkova IV, Byzova NA, Varitsev YA, Zherdev AV, Dzantiev BB. Silver-enhanced lateral flow immunoassay for highly-sensitive detection of potato leafroll virus. FOOD AGR IMMUNOL 2017. [DOI: 10.1080/09540105.2017.1401044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Vasily G. Panferov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda A. Byzova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Yuri A. Varitsev
- A.G. Lorch All-Russian Potato Research Institute, Kraskovo, Moscow region, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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Development of a colorimetric reverse transcription loop-mediated isothermal amplification assay for the detection of Mirafiori lettuce big-vein virus. Arch Virol 2017; 162:2775-2780. [DOI: 10.1007/s00705-017-3404-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 10/19/2022]
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12
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Leptospirosis in Central America: Techniques for Diagnosis and Molecular Characterization. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0106-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Zhao N, Liu J, Sun D. Detection of HCV genotypes 1b and 2a by a reverse transcription loop-mediated isothermal amplification assay. J Med Virol 2017; 89:1048-1054. [PMID: 27935066 DOI: 10.1002/jmv.24747] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) genotypes 1b and 2a are the major cause of liver disease in northern China; however, conventional detection tools are labor-consuming, technically demanding, and costly. Here, we assessed the specificity, sensitivity, and clinical utility of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of HCV genotypes 1b and 2a. Firstly, clinical samples were collected from HCV genotype 1b and 2a infected patients and the RNA were extracted. Secondly, specificity of RT-LAMP assay for detection HCV genotypes 1b and 2a were tested against viral genomes of other hepatitis viruses. Sensitivity of RT-LAMP assay was determined using serial dilutions of standard HCV genotypes 1b and 2a. The amplified products were detected by both electrophoresis and calcein/Mn2+ -dependent visual methods. Finally, we compared the clinical detection rate of RT-LAMP to that of real-time PCR. RT-LAMP assay showed high specificity to detect HCV genotypes 1b and 2b since there was no cross-reactivity with other hepatitis viruses. Sensitivity of RT-LAMP was 100 IU/mL for both genotypes detected by either electrophoresis or calcein/Mn2+ -dependent visual methods. The detection rate of RT-LAMP assay in clinical samples was also comparable to that of real-time PCR without significant difference between the both assays. This study proposes a newly developed RT-LAMP assay for detection of HCV genotypes 1b and 2a. RT-LAMP is highly specific, sensitive, and simple diagnostic tool which would be useful for screening and early diagnosis of HCV especially in resource-limited environments.
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Affiliation(s)
- Na Zhao
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei Province, China.,The Experiment Center of Pathogen Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Jinxia Liu
- The Experiment Center of Pathogen Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Dianxing Sun
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei Province, China
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14
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Banerjee A, Roy S, Sharma SK, Dutta SK, Chandra S, Ngachan SV. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid diagnosis of chilli veinal mottle virus. Arch Virol 2016; 161:1957-61. [PMID: 27063408 DOI: 10.1007/s00705-016-2850-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/28/2016] [Indexed: 10/22/2022]
Abstract
Chilli veinal mottle virus (ChiVMV) causes significant economic loss to chilli cultivation in northeastern India, as well as in eastern Asia. In this study, we have developed a single-tube one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid, sensitive and specific diagnosis of ChiVMV. Amplification could be visualized after adding SYBR Green I (1000×) dye within 60 min under isothermal conditions at 63 °C, with a set of four primers designed based on the large nuclear inclusion protein (NIb) domain of ChiVMV (isolate KC-ML1). The RT-LAMP method was 100 times more sensitive than one-step reverse transcription polymerase chain reaction (RT-PCR), with a detection limit of 0.0001 ng of total RNA per reaction.
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Affiliation(s)
- Amrita Banerjee
- ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793 103, India.
| | - Somnath Roy
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Umiam, Meghalaya, 793 103, India
| | - Susheel Kumar Sharma
- ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat, Manipur, 795 004, India
| | - Sudip Kumar Dutta
- ICAR Research Complex for NEH Region, Mizoram Centre, Kolasib, Mizoram, 796 081, India
| | - Satish Chandra
- ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793 103, India
| | - S V Ngachan
- ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793 103, India
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Reverse transcription loop-mediated isothermal amplification to rapidly detect Rice ragged stunt virus. Saudi J Biol Sci 2016; 25:1577-1584. [PMID: 30581320 PMCID: PMC6302892 DOI: 10.1016/j.sjbs.2016.02.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 11/22/2022] Open
Abstract
Rice ragged stunt virus (RRSV) is a very important virus that infects rice and causes serious yield losses in Asian countries and other major rice planting areas. Thus, it is urgent to establish an efficient and practical approach for identification and diagnosis in the field. Our results indicated that reverse transcription loop-mediated isothermal amplification (RT-LAMP) reactions are more efficient and sensitive than RT-PCR for RRSV detection. The optimal LAMP conditions were as follows: 0.4–1.2 μM internal primers, 0.2–0.25 μM external primers, 0.8 μM loop primers, and incubation at 62 °C or 63 °C for 30 min. Furthermore, the RT-LAMP primers specifically targeted RRSV virus and resulted in typical waterfall-like bands by gel electrophoresis and sigmoidal amplification curves. The primers could not be used to amplify other common plant viruses including Papaya ringspot virus (PRSV), Rice yellow stunt virus (RYSV), Sorghum mosaic virus (SrMV), Cactus virus X (CVX), Melon yellow spot virus (MYSV) and Southern rice black-streaked dwarf virus (SRBSDV). Ten-fold serial dilutions of RRSV cDNA indicated that RT-LAMP is much faster and at least ten times more sensitive than RT-PCR in detecting the virus. The waterfall-like product bands could be observed within one hour. In the field study, about 77% samples were identified as RRSV. RT-LAMP has many benefits over RT-PCR such as low cost and high accuracy, sensitivity, and specificity. This technology meets the requirements for rapid diagnosis of plant virus diseases in the field to best guide management practices for growers.
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Development of a Rapid Method for the Visible Detection of Pork DNA in Halal Products by Loop-Mediated Isothermal Amplification. FOOD ANAL METHOD 2015. [DOI: 10.1007/s12161-015-0246-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Almasi MA, Aghapour-Ojaghkandi M, Bagheri K, Ghazvini M, Hosseyni-Dehabadi SM. Comparison and evaluation of two diagnostic methods for detection of npt II and GUS genes in Nicotiana tabacum. Appl Biochem Biotechnol 2015; 175:3599-616. [PMID: 25820356 DOI: 10.1007/s12010-015-1529-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 01/26/2015] [Indexed: 11/24/2022]
Abstract
To diminish the time required for some diagnostic assays including polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP) and also a visual detection protocol on the basis of npt II and GUS genes in transgenic tobacco plants were used. Agrobacterium tumefaciens-mediated transformation of Nicotiana tabacum leaf discs was performed with plant transformation vector of pBI 121. From kanamycin-resistant plants selected by their antibiotic resistance, four plants were selected for DNA isolation. Presence of the transgene was confirmed in the transformants by PCR and LAMP. In this regard, all LAMP and PCR primers were designed on the basis of the gene sequences of npt II and GUS. The LAMP assay was applied for direct detection of gene marker from plant samples without DNA extraction steps (direct LAMP assay). Also, a novel colorimetric LAMP assay for rapid and easy detection of npt II and GUS genes was developed here, its potential compared with PCR assay. The LAMP method, on the whole, had the following advantages over the PCR method: easy detection, high sensitivity, high efficiency, simple manipulation, safety, low cost, and user friendly.
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Affiliation(s)
- Mohammad Amin Almasi
- Young Researchers and Elite Club, North Tehran Branch, Islamic Azad University, Tehran, Iran,
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Zhao LM, Li G, Gao Y, Zhu YR, Liu J, Zhu XP. Reverse transcription loop-mediated isothermal amplification assay for detecting tomato chlorosis virus. J Virol Methods 2014; 213:93-7. [PMID: 25486081 DOI: 10.1016/j.jviromet.2014.11.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 11/10/2014] [Accepted: 11/18/2014] [Indexed: 10/24/2022]
Abstract
A betaine-free reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed and optimised for detecting tomato chlorosis virus (ToCV), one of the most important viruses that infect tomato crops worldwide. A set of four specific primers was designed against the RNA-dependent RNA polymerase (RdRp) gene. The betaine-free RT-LAMP procedure could be completed within 40 min under isothermal conditions at 60 °C without a thermal cycler, and no cross-reactivity was seen with other tomato viral pathogens. Sensitivity analysis showed that RT-LAMP could detect viral dilutions up to 2.0×10(-7)ng, which is 100-times more sensitive than reverse transcription-polymerase chain reaction (RT-PCR). In addition, naked-eye observation after staining in-tube RT-LAMP products with SYBR Green I facilitated detection of ToCV by avoiding the requirement for ethidium staining following gel electrophoresis. These results suggest that ToCV RT-LAMP is a rapid, sensitive, and affordable diagnostic tool that is more suitable than RT-PCR for the detection and surveillance of ToCV in field samples.
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Affiliation(s)
- Li-ming Zhao
- State Key Laboratory of Crop Biology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Ying Gao
- State Key Laboratory of Crop Biology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - You-rong Zhu
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jin Liu
- State Key Laboratory of Crop Biology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xiao-ping Zhu
- State Key Laboratory of Crop Biology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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Shen W, Tuo D, Yan P, Yang Y, Li X, Zhou P. Reverse transcription loop-mediated isothermal amplification assay for rapid detection of Papaya ringspot virus. J Virol Methods 2014; 204:93-100. [PMID: 24769198 DOI: 10.1016/j.jviromet.2014.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/10/2014] [Accepted: 04/15/2014] [Indexed: 11/16/2022]
Abstract
Papaya ringspot virus (PRSV) and Papaya leaf distortion mosaic virus (PLDMV), which causes disease symptoms similar to PRSV, threaten commercial production of both non-transgenic-papaya and PRSV-resistant transgenic papaya in China. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect PLDMV was developed previously. In this study, the development of another RT-LAMP assay to distinguish among transgenic, PRSV-infected and PLDMV-infected papaya by detection of PRSV is reported. A set of four RT-LAMP primers was designed based on the highly conserved region of the P3 gene of PRSV. The RT-LAMP method was specific and sensitive in detecting PRSV, with a detection limit of 1.15×10(-6)μg of total RNA per reaction. Indeed, the reaction was 10 times more sensitive than one-step RT-PCR. Field application of the RT-LAMP assay demonstrated that samples positive for PRSV were detected only in non-transgenic papaya, whereas samples positive for PLDMV were detected only in commercialized PRSV-resistant transgenic papaya. This suggests that PRSV remains the major limiting factor for non-transgenic-papaya production, and the emergence of PLDMV threatens the commercial transgenic cultivar in China. However, this study, combined with the earlier development of an RT-LAMP assay for PLDMV, will provide a rapid, sensitive and cost-effective diagnostic power to distinguish virus infections in papaya.
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Affiliation(s)
- Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology & Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology & Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology & Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yong Yang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology & Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology & Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology & Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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20
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Shen W, Tuo D, Yan P, Li X, Zhou P. Detection of Papaya leaf distortion mosaic virus by reverse-transcription loop-mediated isothermal amplification. J Virol Methods 2013; 195:174-9. [PMID: 24100065 DOI: 10.1016/j.jviromet.2013.09.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/10/2013] [Accepted: 09/20/2013] [Indexed: 11/24/2022]
Abstract
Papaya leaf distortion mosaic virus (PLDMV) can infect transgenic papaya resistant to a related pathogen, Papaya ringspot virus (PRSV), posing a substantial threat to papaya production in China. Current detection methods, however, are unable to be used for rapid detection in the field. Here, a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of PLDMV, using a set of four RT-LAMP primers designed based on the conserved sequence of PLDMV CP. The RT-LAMP method detected specifically PLDMV and was highly sensitive, with a detection limit of 1.32×10(-6) μg of total RNA per reaction. Indeed, the reaction was 10 times more sensitive than one-step RT-PCR, while also requiring significantly less time and equipment. The effectiveness of RT-LAMP and one-step RT-PCR in detecting the virus were compared using 90 field samples of non-transgenic papaya and 90 field samples of commercialized PRSV-resistant transgenic papaya from Hainan Island. None of the non-transgenic papaya tested positive for PLDMV using either method. In contrast, 19 of the commercialized PRSV-resistant transgenic papaya samples tested positive by RT-LAMP assay, and 6 of those tested negative by RT-PCR. Therefore, the PLDMV-specific RT-LAMP is a simple, rapid, sensitive, and cost-effective tool in the field diagnosis and control of PLDMV.
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Affiliation(s)
- Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology & Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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