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Kalaiponmani K, Parameswari B, Tripathi A, Celia Chalam V. Development of simplex and quintuplex RT-PCR for simultaneous detection of soybean viruses. J Virol Methods 2024; 330:115010. [PMID: 39222751 DOI: 10.1016/j.jviromet.2024.115010] [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: 04/03/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Five simplex and a multiplex-RT-PCR (m-RT-PCR) protocols were developed for detection and differentiation of bean pod mottle virus (BPMV), cherry leaf roll virus (CLRV), raspberry ringspot virus (RpRSV), soybean mosaic virus (SMV) and tomato ringspot virus (ToRSV) infecting soybean. The simplex RT-PCR protocols produced virus-specific amplicons of 538 bp for BPMV, 139 bp for CLRV, 298 bp for RpRSV, 403 bp for SMV, and 282 bp for ToRSV, with sensitivity down to 10-4 diluted cDNA. Further, to detect all the five viruses simultaneously in a single tube a quintuplex RT-PCR protocol was optimized with as low as 10-3 diluted cDNA and 0.05 µM primer. To validate the reliability of the simplex RT-PCR protocol, imported soybean samples were tested by ELISA as well as RT-PCR. The results revealed that the developed protocol could detect the viruses in imported soybean, and found to be efficient than ELISA in resolving ambiguity in detection of seed borne viruses. The developed simplex and quintuplex RT-PCR protocol will be quite helpful for the diagnosis of soybean germplasm co-infected with viruses during the quarantine processing for ensuring virus free long term seed conservation in the National Gene Bank as well as for quarantine certification.
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Affiliation(s)
- K Kalaiponmani
- Division of Plant Quarantine, ICAR-NBPGR, New Delhi, India.
| | | | - A Tripathi
- Division of Plant Quarantine, ICAR-NBPGR, New Delhi, India
| | - V Celia Chalam
- Division of Plant Quarantine, ICAR-NBPGR, New Delhi, India.
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Raigond B, Pathania S, Verma G, Bhardwaj P, Kochhar T, Chakrabarti SK. Development and application of reverse transcription-loop mediated isothermal amplification assay for sensitive detection of groundnut bud necrosis virus infecting potato. Virology 2023; 587:109872. [PMID: 37657354 DOI: 10.1016/j.virol.2023.109872] [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: 05/23/2023] [Revised: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023]
Abstract
Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of groundnut bud necrosis virus (GBNV) causing potato stem necrosis disease. The isothermal temperatures, reaction periods and concentrations of reaction mixture were optimized where, the assay worked well at 65 °C for 50 min, 6 U of WarmStart Bst 2.0 DNA polymerase, 1.4 mM dNTPs and 2.0 mM MgSO4. The optimized assay proved to be specific to GBNV with no cross reactivity to other viruses infecting potato in India. The specificity of RT-LAMP assay was found to be 100 fold more sensitive than that of RT-PCR. The developed assay was applied for the detection of GBNV from 80 potato leaf samples where 24 samples were found infected which was confirmed by RT-PCR. It was concluded that the RT-LAMP assay developed for detection of GBNV was specific, sensitive and suitable for its use in virus indexing under potato seed production programme.
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Affiliation(s)
- Baswaraj Raigond
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India; Center on Rabi Sorghum, ICAR-Indian Institute of Millets Research, Regional Station, Solapur, Maharashtra, 413006, India.
| | - Shruti Pathania
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Gaurav Verma
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Pooja Bhardwaj
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Tarvinder Kochhar
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - S K Chakrabarti
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
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3
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Ren J, Zhang J, Wang Q, Zhou Y, Wang J, Ran C, Shang Q. Molecular characterization of strawberry vein banding virus from China and the development of loop‑mediated isothermal amplification assays for their detection. Sci Rep 2022; 12:4912. [PMID: 35318413 PMCID: PMC8940885 DOI: 10.1038/s41598-022-08981-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
Abstract
Strawberry vein banding virus (SVBV) is one of the serious viral pathogens infecting strawberry worldwide. To understand the molecular characterization of SVBV from China, complete genome sequences of sixteen SVBV isolates were cloned and sequenced. Sequence comparison showed they shared high nucleotide sequence identity (93.6–99.5%) with isolates from China and Japan (96.6–98.4%), while relatively low identity with the isolates from Canada (91.9–93.7%) and USA (85.5–85.9%). Phylogenetic analyses based on the complete genome sequence or coat protein (CP) gene showed the SVBV isolates clustered into three clades correlated with geographic distribution. Recombination analyses identified 13 recombinants and 21 recombinant events, indicating frequent and multiple recombinations in SVBV evolution. Furthermore, a sensitive loop-mediated isothermal amplification (LAMP) method was developed for rapid detection of SVBV isolates, which could be especially suitable for seedling propagation, virus-free culture and routine diagnostics in field investigation. This study offers new understanding of the molecular evolution and may help to improve the management of SVBV.
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Affiliation(s)
- Junda Ren
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing, 102206, China
| | - Jiaxing Zhang
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing, 102206, China
| | - Qiushi Wang
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing, 102206, China
| | - Yu Zhou
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing, 102206, China
| | - Jingxuan Wang
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing, 102206, China
| | - Ce Ran
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing, 102206, China
| | - Qiaoxia Shang
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Department of Plant Protection, Beijing University of Agriculture, Beijing, 102206, China.
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Tahzima R, Foucart Y, Peusens G, Reynard JS, Massart S, Beliën T, De Jonghe K. An Advanced One-Step RT-LAMP for Rapid Detection of Little cherry virus 2 Combined with High-Throughput Sequence-Based Phylogenomics Reveal Divergent Flowering Cherry Isolates. PLANT DISEASE 2022; 106:835-845. [PMID: 34546772 DOI: 10.1094/pdis-03-21-0677-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Little cherry virus 2 (LChV-2, genus Ampelovirus) is considered to be the main causal agent of the economically damaging little cherry disease, which can only be controlled by removal of infected trees. The widespread viral disease of sweet cherry (Prunus avium L.) is affecting the survival of long-standing orchards in North America and Europe, hence the dire need for an early and accurate diagnosis to establish a sound disease control strategy. The endemic presence of LChV-2 is mainly confirmed using laborious time-consuming reverse-transcription (RT-PCR). A rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay targeting a conserved region of the coat protein was developed and compared with conventional RT-PCR for the specific detection of LChV-2. This affordable assay, combined with a simple RNA extraction, deploys desirable characteristics such as higher ability for faster (<15 min), more analytically sensitive (100-fold), and robust broad-range diagnosis of LChV-2 isolates from sweet cherry, ornamental flowering cherry displaying heterogenous viral etiology and, for the first time, newly identified potential insect vectors. Moreover, use of Sanger and total RNA high-throughput sequencing as complementary metaviromics approaches confirmed the LChV-2 RT-LAMP detection of divergent LChV-2 isolates in new hosts and the relationship of their whole-genome was exhaustively inferred using maximum-likelihood phylogenomics. This entails unprecedented critical understanding of a novel evolutionary clade further expanding LChV-2 viral diversity. In conclusion, this highly effective diagnostic platform facilitates strategical support for early in-field testing to reliably prevent dissemination of new LChV-2 outbreaks from propagative plant stocks or newly postulated insect vectors. Validated results and major advantages are herein thoroughly discussed, in light of the knowledge required to increase the potential accuracy of future diagnostics and the essential epidemiological considerations to proactively safeguard cherries and Prunus horticultural crop systems from little cherry disease.
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Affiliation(s)
- Rachid Tahzima
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
- Department of Integrated and Urban Phytopathology, Gembloux Agro-BioTech, University of Liège, 5030 Gembloux, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Gertie Peusens
- Department of Zoology, Proefcentrum Fruitteelt vzw, 3800 Sint-Truiden, Belgium
| | | | - Sébastien Massart
- Department of Integrated and Urban Phytopathology, Gembloux Agro-BioTech, University of Liège, 5030 Gembloux, Belgium
| | - Tim Beliën
- Department of Zoology, Proefcentrum Fruitteelt vzw, 3800 Sint-Truiden, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
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Yang QQ, Zhao XX, Wang D, Zhang PJ, Hu XN, Wei S, Liu JY, Ye ZH, Yu XP. A reverse transcription-cross-priming amplification method with lateral flow dipstick assay for the rapid detection of Bean pod mottle virus. Sci Rep 2022; 12:681. [PMID: 35027575 PMCID: PMC8758742 DOI: 10.1038/s41598-021-03562-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022] Open
Abstract
Bean pod mottle virus (BPMV) is a destructive virus that causes serious economic losses in many countries every year, highlighting the importance of its effective detection. In this study, we developed a fast reverse transcription-cross-priming amplification (RT-CPA) coupled with lateral flow dipstick (LFD) diagnostic method for BPMV detection. The RT-CPA-LFD assay that targets the coat protein gene of BPMV was highly specific against diagnosing four other common viruses transmitted by soybean seeds, i.e., Southern bean mosaic virus (SBMV), Tomato ringspot virus (ToRSV), Arabis mosaic virus (ArMV), and Tobacco ringspot virus (TRSV). The sensitivities of the real-time fluorescent RT-CPA and the RT-CPA-LFD assay were at least 50 pg/μl and 500 pg/μl, respectively. Despite a compromise in the limit of detection of the RT-CPA method compared with TaqMan-MGB real-time RT-PCR, our results demonstrated a notably better performance in the detection of field samples of BPMV-infested soybean seeds. With the advantages of efficiency and convenience by visual determination, the RT-CPA-LFD assay presents a potential application for the rapid and accurate detection of BPMV in routine tests.
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Affiliation(s)
- Qian-Qian Yang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China.
| | - Xing-Xing Zhao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Dao Wang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Peng-Jun Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xue-Nan Hu
- Guangzhou Customs Technology Center, Guangzhou, China
| | - Shuang Wei
- Guangzhou Customs Technology Center, Guangzhou, China
| | | | - Zi-Hong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiao-Ping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China.
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Li X, Hu W, Li Y, Li Y, Chen S, Wang J. Development of an RT-LAMP assay for the detection of maize yellow mosaic virus in maize. J Virol Methods 2021; 300:114384. [PMID: 34856307 DOI: 10.1016/j.jviromet.2021.114384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/12/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Maize is one of the most widely cultivated cereal crops worldwide. Maize yellow mosaic virus (MaYMV) (species Maize yellow mosaic virus, genus Polerovirus and family Luteoviridae) was first reported in maize from China. In this study, a one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting MaYMV. The optimal concentrations of betaine, Mg2+ and dNTPs for the assay were 0 M, 1.4 mM and 6 mM, respectively, and the optimal reaction time was 50 min. Using total plant RNA as the template, the detection limit of the RT-LAMP assay for MaYMV was 1 pg, while that of RT-PCR was 100 pg, indicating that the RT-LAMP assay developed was 100 times more sensitive than RT-PCR. Importantly, the RT-LAMP assay successfully detected MaYMV using rapidly extracted crude RNA from infected maize as a template. In conclusion, the RT-LAMP assay developed was a rapid, specific, sensitive and low-cost method for the detection of MaYMV in field samples of maize.
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Affiliation(s)
- Xiaoqin Li
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Wenli Hu
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Yu Li
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Yan Li
- Yunnan Plant Protection and Quarantine Station, Kunming, 650034, China
| | - Suiyun Chen
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Jianguang Wang
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China.
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7
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Kwon SJ, Cho YE, Kim MH, Seo JK. A one-step reverse-transcription loop-mediated isothermal amplification assay optimized for the direct detection of cucumber green mottle mosaic virus in cucurbit seeds. Mol Cell Probes 2021; 60:101775. [PMID: 34673202 DOI: 10.1016/j.mcp.2021.101775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022]
Abstract
Cucumber green mottle mosaic virus (CGMMV) is a seed-borne virus that causes significant economic losses in farms cultivating cucurbit plants. With the increase in global trade of cucurbit seeds, it is essential to develop a rapid, reliable, and convenient diagnostic method for the direct detection of CGMMV in these seeds for prevention and management of the disease. Here, we developed a one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the direct detection of CGMMV in cucurbit seeds. To improve the efficiency of the one-step RT-LAMP assay, six primers were designed to target the most conserved regions of the gene encoding the movement protein of CGMMV. Our one-step RT-LAMP assay was optimized to improve specificity and sensitivity for CGMMV detection in individual seeds. A comparison of the detection sensitivity revealed that our one-step RT-LAMP assay was 100-fold more sensitive than the current reverse transcription-polymerase chain reaction assay used for CGMMV quarantine in Korea. Collectively, the one-step RT-LAMP assay developed in the present study is appropriate for the direct detection of CGMMV in individual cucurbit seeds.
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Affiliation(s)
- Sun-Jung Kwon
- Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea.
| | - Young-Eun Cho
- Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Myung-Hwi Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jang-Kyun Seo
- Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea; Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Department of International Agricultural Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea.
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Kumar R, Kaundal P, Arjunan J, Sharma S, Chakrabarti SK. Development of a visual detection method for Potato virus S by reverse transcription loop-mediated isothermal amplification. 3 Biotech 2020; 10:213. [PMID: 32351871 PMCID: PMC7182647 DOI: 10.1007/s13205-020-02214-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
A reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay was developed to detect the Potato virus S (PVS) in potato. Two sets of six novel primers that recognize the coat protein gene sequence of the PVS were designed and RT-LAMP assay was optimized for the parameters such as different concentrations of primers, MgSO4, betaine, dNTPs, Bst DNA polymerase, temperature and duration. The RT-LAMP was carried out under isothermal conditions without the thermal cycler using PVS infected leaf and tuber samples, LAMP specific primers with amplification at 65 °C for 60 min, and 80 °C for 5 min. The results were assessed by gel electrophoresis and visual observation of colour change using SYBR Green I dye. The detection limit of the developed RT-LAMP assay was determined and compared with a conventional reverse transcription-polymerase chain reaction (RT-PCR). RT-LAMP was found 100 times more sensitive than RT-PCR. The optimized RT-LAMP assay is robust, reliable, sensitive and convenient for the detection of the PVS in infected potato tubers including asymptomatic plants. No cross-reactions were observed with healthy plants and other potato viruses. The assay is economical and can be employed in large scale testing of potato plants against PVS under healthy seed potato production programme.
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Affiliation(s)
- Ravinder Kumar
- 1ICAR-Central Potato Research Institute, Shimla, HP 171 001 India
| | - Priyanka Kaundal
- 1ICAR-Central Potato Research Institute, Shimla, HP 171 001 India
| | - Jeevalatha Arjunan
- 2ICAR-Indian Institute of Spices Research, Marikunnu P.O., Kozhikode, Kerala 673 012 India
| | - Sanjeev Sharma
- 1ICAR-Central Potato Research Institute, Shimla, HP 171 001 India
| | - S K Chakrabarti
- 1ICAR-Central Potato Research Institute, Shimla, HP 171 001 India
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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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Jiao Y, Xu C, Li J, Gu Y, Xia C, Xie Q, Xie Y, An M, Xia Z, Wu Y. Characterization and a RT-RPA assay for rapid detection of Chilli Veinal mottle virus (ChiVMV) in tobacco. Virol J 2020; 17:33. [PMID: 32156292 PMCID: PMC7065361 DOI: 10.1186/s12985-020-01299-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chilli veinal mottle virus (ChiVMV), which belongs to the genus Potyvirus of the family Potyviridae, mainly infects solanaceous plants and has caused serious economic losses in Asia and Africa. Tobacco plants infected with ChiVMV suffered from punctate necrosis of leaves, leaf deformation, systemic necrosis of leaves and stems, and eventually plant death. However, ChiVMV infection could not usually be identified given the lack of rapid and efficient detection assays in tobacco plants. Therefore, an isolate of tobacco-infecting ChiVMV (ChiVMV-LZ) was obtained, and a novel isothermal amplification and detection technique, reverse transcription-recombinase polymerase amplification (RT-RPA), was established to detect ChiVMV in tobacco plants. METHODS In this study, the full-length genome of ChiVMV-LZ was obtained using reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) assays. The genome sequence of ChiVMV-LZ was characterized by sequence alignment and phylogenetic analysis. Then, a RT-RPA assay was established for rapid and sensitive detection of ChiVMV-LZ in tobacco. Additionally, the established RT-RPA assay was compared to the RT-PCR assay in aspect of sensitivity and application in field-collected tobacco samples. RESULTS ChiVMV-LZ was isolated from diseased tobacco in Luzhou, Sichuan, China. The tobacco plants inoculated with ChiVMV-LZ showed typical symptoms of yellow and round spots on the leaves, and curled and folded leaf margin, similar to those observed on naturally ChiVMV-infected tobacco in the field. The full-length genomic sequence of ChiVMV-LZ was determined to be 9742 nucleotides. Sequence alignment and phylogenetic analysis showed that ChiVMV-LZ was most closely related to ChiVMV-Yp8 isolated from pepper plants in Sichuan province while distantly related to ChiVMV-YN from tobacco in Yunnan province, indicating a possibly geographical differentiation of ChiVMV isolates. Additionally, a RT-RPA assay was established for rapid detection of ChiVMV in tobacco. The RT-RPA has no cross-reaction with other related tobacco viruses and is about 10-fold more sensitive than conventional RT-PCR method. CONCLUSION The characterization of ChiVMV-LZ infecting tobacco was determined, and the established RT-RPA assay provides a reliable and effective method for rapid detection of ChiVMV in tobacco.
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Affiliation(s)
- Yubing Jiao
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Chuantao Xu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
- Luzhou City Company of Sichuan Tobacco Company, Luzhou, 646000, China
| | - Jialun Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yong Gu
- Luzhou City Company of Sichuan Tobacco Company, Luzhou, 646000, China
| | - Chun Xia
- Luzhou City Company of Sichuan Tobacco Company, Luzhou, 646000, China
| | - Qiang Xie
- Luzhou City Company of Sichuan Tobacco Company, Luzhou, 646000, China
| | - Yunbo Xie
- Sichuan Province Company of China Tobacco Corporation, Chengdu, 610041, China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China.
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11
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Wan J, Guo J, Lu Z, Bie X, Lv F, Zhao H. Development of a test kit for visual loop-mediated isothermal amplification of Salmonella in spiked ready-to-eat fruits and vegetables. J Microbiol Methods 2019; 169:105830. [PMID: 31891738 DOI: 10.1016/j.mimet.2019.105830] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 12/25/2019] [Accepted: 12/27/2019] [Indexed: 02/02/2023]
Abstract
The purpose of this study was to assemble two types of loop-mediated isothermal amplification (LAMP) kit that have the ability to visually detect Salmonella in ready-to-eat fruits and vegetables. The reaction results were obtained within 20-40 min after addition of DNA and can be discerned by the naked eye or an amplification plot. The stability of the LAMP wet kit was evident after multiple freezing and thawing cycles, and the one-step LAMP lyophilized kit was further evolved to allow ambient temperature transport for deployment in resource-limited settings. The cost-effective wet kit had the ability to detect minimum amounts of 1.8 CFU/ml Salmonella DNA without enrichment, while the sensitivity of the one-step LAMP lyophilized kit was only 9.8 × 103 CFU/ml. They both have good anti-interference, as they were both able to detect 2.1 × 102 CFU/ml Salmonella mixed with 106 CFU/ml four non-Salmonella strain mixture. Moreover, cucumber and lettuce that were contaminated with an initial inoculation of 1.7 CFU of Salmonella/10 g showed detection within a reaction time of 30 min after 10 h enrichment. The present research setup is a convenient and practical kit for Salmonella rapid detection that has good application prospects in food safety monitoring.
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Affiliation(s)
- Jiajia Wan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Jianping Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
| | - Fengxia Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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12
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One-step reverse transcription loop-mediated isothermal amplification: a simple, sensitive and rapid assay for detection of potato virus X in potato leaves and tubers. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42360-019-00147-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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13
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Tahzima R, Foucart Y, Peusens G, Beliën T, Massart S, De Jonghe K. New sensitive and fast detection of Little cherry virus 1 using loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2018; 265:91-98. [PMID: 30593838 DOI: 10.1016/j.jviromet.2018.12.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 11/20/2018] [Accepted: 12/26/2018] [Indexed: 12/26/2022]
Abstract
Little cherry virus 1 (LChV-1) belongs to the genus Velarivirus, family Closteroviridae, is an economically important pathogen affecting mainly cherry around the world emphasizing the impetus for its efficient and accurate on-site detection. This study describes the development of a reliable diagnostic protocol of LChV-1 based on a one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP). The protocol detects LChV-1 isolates in less than 10 min by fluorescence monitoring using a mobile detection device and is most optimal when performed at 67 °C. Sharp melting curves and unique melting temperatures (Tm) were obtained for the positive samples. Both the RT-LAMP and classical RT-PCR methods are capable of specifically detecting LChV-1 in infected leaf tissues. In addition, the RT-LAMP has remarkable advantages in comparison to RT-PCR. It is at least hundred fold more sensitive, significantly faster (allowing on-field leaf-to-result diagnostic) and efficient at minimal cost. In conclusion, this innovative RT-LAMP approach can contribute to the implementation of sustainable integrated management strategies for detection of LChV-1 in commercial orchards or for horticultural research stations. It is also suitable for decision support in phytosanitary epidemiological programs.
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Affiliation(s)
- Rachid Tahzima
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; Laboratory of Integrated and Urban Phytopathology, University of Liège (ULg), Gembloux Agro-Bio tech, 5030 Gembloux, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Gertie Peusens
- Department of Zoology, Proefcentrum Fruitteelt (pcfruit), 3800 Sint-Truiden, Belgium
| | - Tim Beliën
- Department of Zoology, Proefcentrum Fruitteelt (pcfruit), 3800 Sint-Truiden, Belgium
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, University of Liège (ULg), Gembloux Agro-Bio tech, 5030 Gembloux, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium.
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14
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Meena PN, Kharbikar LL, Rana RS, Satpathy S, Shanware A, Sivalingam PN, Nandanwar S. Detection of Mesta yellow vein mosaic virus (MeYVMV) in field samples by a loop-mediated isothermal amplification reaction. J Virol Methods 2018; 263:81-87. [PMID: 30359678 DOI: 10.1016/j.jviromet.2018.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 10/05/2018] [Accepted: 10/20/2018] [Indexed: 10/28/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) assay was optimized for the detection of Mesta yellow vein mosaic virus (MeYVMV) in diseased plants of mesta (Hibiscus sabdariffa L.& H. cannabinus L.). The LAMP assay was optimized using a set of six primers targeting the MeYVMV genome and could be completed in 30-60 min at 63 °C. The LAMP amplification results were visualized by adding 1 μl of hydroxy naphthol blue (HNB) dye in a 25 μl LAMP reaction mixture prior to amplification as well as by electrophoresis. The LAMP assay, which detected MeYVMV in a 10-5-fold diluted total DNA, was more sensitive than the PCR assay (10-4-fold dilution). The optimized LAMP assay was able to detect MeYVMV in different parts of the kenaf and roselle plants. Similarly, the optimized PCR assay was also capable of detecting MeYVMV in all the different parts of the kenaf plant but failed to detect the virus in the stem and flower buds of the roselle plant. Validation of the LAMP and LAMP with HNB dye assays revealed that the optimized reactions can be used successfully for the in-situ detection of MeYVMV in field samples and in virus quarantine programs. This is the first report of the detection of the begomovirus species, MeYVMV, in the mucilaginous plant species, kenaf and roselle, using a LAMP assay.
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Affiliation(s)
- Prabhu Narayan Meena
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700120, India.
| | - Lalit Laxman Kharbikar
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700120, India; ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, 493225, India.
| | - Rajeev Singh Rana
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700120, India.
| | - Subrata Satpathy
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700120, India.
| | - Arti Shanware
- Rajiv Gandhi Biotechnology Centre, RTM Nagpur University, Nagpur, 440033, India.
| | | | - Shweta Nandanwar
- Harper Adams University, Newport, Shropshire, TF10 8NB, United Kingdom.
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15
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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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16
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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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17
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Zhu M, Zhang WN, Tian JY, Zhao WY, Chen ZQ, Sun LH, Xue F, Liu Y, Tan XQ, Wang LM, Liu FQ, Tao XR. Development of a lateral-flow assay (LFA) for rapid detection of Soybean mosaic virus. J Virol Methods 2016; 235:51-57. [PMID: 27235541 DOI: 10.1016/j.jviromet.2016.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 05/02/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022]
Abstract
Soybean mosaic virus (SMV) is the most common virus in soybean and poses a serious threat to crop production and germplasm recession in many countries worldwide. In this study, a highly practical and rapid lateral-flow assay (LFA) was developed for the detection of SMV. The SMV coat protein (CP) was prokaryotically expressed and purified to immunize mice. After generation of hybridoma cell lines, four anti-SMV monoclonal antibodies were selected. The LFA-strip was then assembled using a double-antibody sandwich strategy. When the SMV-infected leaf sample was assayed using the assembled LFA-strip, the positive pink color appeared in the test line within 5-10min. The strip only gave positive results with SMV and not other viruses tested and could be used to detect 800 fold dilutions of infected leaf samples. The LFA could be used to detect SMV in infected leaf tissue as well as soybean seeds. To our knowledge, this is the first report of the development of a LFA for the detection of SMV. The practical, rapid and specific assay that was developed in this study can be widely applied to the diagnosis and surveillance of SMV in the laboratory and the field.
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Affiliation(s)
- Min Zhu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen-Na Zhang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin-Yan Tian
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen-Yang Zhao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zheng-Qiang Chen
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Li-Hua Sun
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fan Xue
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yong Liu
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Xin-Qiu Tan
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Li-Min Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng-Quan Liu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao-Rong Tao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China.
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18
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Budziszewska M, Wieczorek P, Obrępalska-Stęplowska A. One-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) for detection of tomato torrado virus. Arch Virol 2016; 161:1359-64. [PMID: 26887971 PMCID: PMC4839060 DOI: 10.1007/s00705-016-2774-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/26/2016] [Indexed: 11/27/2022]
Abstract
'Torrado' disease caused by tomato torrado virus (ToTV) is responsible for considerable losses in tomato production. Therefore, a one-step reverse transcription loop-mediated isothermal amplification protocol for early and fast detection of ToTV isolates has been developed. The RNA extracted from ToTV-infected plants was tested using this protocol with a set of six primers specific for the Vp35 coat protein gene sequence. The amplified products were analyzed using amplification curves, electrophoresis, and direct staining of DNA. The sensitivity of the protocol was tenfold higher than that of conventional RT-PCR. This new protocol is inexpensive, rapid, simple, and very sensitive.
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Affiliation(s)
- Marta Budziszewska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection-National Research Institute, Władysława Wegorka 20, 60-318, Poznan, Poland
| | - Przemysław Wieczorek
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection-National Research Institute, Władysława Wegorka 20, 60-318, Poznan, Poland
| | - Aleksandra Obrępalska-Stęplowska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection-National Research Institute, Władysława Wegorka 20, 60-318, Poznan, Poland.
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19
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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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20
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Jeong J, Cho SY, Lee WH, Lee KJ, Ju HJ. Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification. THE PLANT PATHOLOGY JOURNAL 2015; 31:219-25. [PMID: 26361470 PMCID: PMC4564147 DOI: 10.5423/ppj.oa.03.2015.0044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/05/2015] [Accepted: 05/10/2015] [Indexed: 05/10/2023]
Abstract
The primary step for efficient control of viral diseases is the development of simple, rapid, and sensitive virus detection. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been used to detect viral RNA molecules because of its simplicity and high sensitivity for a number of viruses. RT-LAMP for the detection of Potato virus X (PVX) was developed and compared with conventional reverse transcription polymerase chain reaction (RT-PCR) to demonstrate its advantages over RT-PCR. RT-LAMP reactions were conducted with or without a set of loop primers since one out of six primers showed PVX specificity. Based on real-time monitoring, RT-LAMP detected PVX around 30 min, compared to 120 min for RT-PCR. By adding a fluorescent reagent during the reaction, the extra step of visualization by gel electrophoresis was not necessary. RT-LAMP was conducted using simple inexpensive instruments and a regular incubator to evaluate whether RNA could be amplified at a constant temperature instead of using an expensive thermal cycler. This study shows the potential of RT-LAMP for the diagnosis of viral diseases and PVX epidemiology because of its simplicity and rapidness compared to RT-PCR.
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Affiliation(s)
- Joojin Jeong
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
| | - Sang-Yun Cho
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
| | - Wang-Hyu Lee
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
| | - Kui-jae Lee
- Division of Biotechnology, Chonbuk National University, Iksan 570-752,
Korea
- Plant Medicinal Research Center, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
- Plant Medicinal Research Center, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
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21
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Rapid detection of Prunus necrotic ringspot virus using magnetic nanoparticle-assisted reverse transcription loop-mediated isothermal amplification. J Virol Methods 2014; 208:85-9. [DOI: 10.1016/j.jviromet.2014.07.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/21/2014] [Accepted: 07/29/2014] [Indexed: 11/21/2022]
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22
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Lang JM, Langlois P, Nguyen MHR, Triplett LR, Purdie L, Holton TA, Djikeng A, Vera Cruz CM, Verdier V, Leach JE. Sensitive detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by loop-mediated isothermal amplification. Appl Environ Microbiol 2014; 80:4519-30. [PMID: 24837384 PMCID: PMC4148787 DOI: 10.1128/aem.00274-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 05/06/2014] [Indexed: 11/20/2022] Open
Abstract
Molecular diagnostics for crop diseases can enhance food security by enabling the rapid identification of threatening pathogens and providing critical information for the deployment of disease management strategies. Loop-mediated isothermal amplification (LAMP) is a PCR-based tool that allows the rapid, highly specific amplification of target DNA sequences at a single temperature and is thus ideal for field-level diagnosis of plant diseases. We developed primers highly specific for two globally important rice pathogens, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) disease, and X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak disease (BLS), for use in reliable, sensitive LAMP assays. In addition to pathovar distinction, two assays that differentiate X. oryzae pv. oryzae by African or Asian lineage were developed. Using these LAMP primer sets, the presence of each pathogen was detected from DNA and bacterial cells, as well as leaf and seed samples. Thresholds of detection for all assays were consistently 10(4) to 10(5) CFU ml(-1), while genomic DNA thresholds were between 1 pg and 10 fg. Use of the unique sequences combined with the LAMP assay provides a sensitive, accurate, rapid, simple, and inexpensive protocol to detect both BB and BLS pathogens.
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Affiliation(s)
- Jillian M. Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | - Paul Langlois
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | | | - Lindsay R. Triplett
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | - Laura Purdie
- Biosciences eastern and central Africa, Nairobi, Kenya
| | | | | | | | - Valérie Verdier
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs, IRD-CIRAD-UM2, Montpellier, France
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
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23
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Anthony Johnson A, Dasgupta I, Sai Gopal D. Development of loop-mediated isothermal amplification and SYBR green real-time PCR methods for the detection of Citrus yellow mosaic badnavirus in citrus species. J Virol Methods 2014; 203:9-14. [DOI: 10.1016/j.jviromet.2014.03.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 02/14/2014] [Accepted: 03/14/2014] [Indexed: 11/25/2022]
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24
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Li X, Zhou Y, Ji H, Xu Z, Zhu L. One-step reverse transcription-loop-mediated isothermal amplification assay for sensitive and rapid detection of porcine kobuvirus. J Virol Methods 2014; 207:1-5. [PMID: 24972366 DOI: 10.1016/j.jviromet.2014.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/09/2014] [Accepted: 06/17/2014] [Indexed: 10/25/2022]
Abstract
Porcine kobuvirus (PKoV) is associated with swine gastroenteritis, but its pathogenesis is uncertain. In this study, a rapid one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) method for the detection of PKoV is developed. A set of four primers specific to six regions within the PKoV 3D gene was designed for the RT-LAMP assay using total RNA extracted from PKoV-infected tissues. The reaction temperature and time for this assay were optimized. Compared with reverse-transcription PCR, RT-LAMP was able to detect PKoV at a 100-fold lower dilution. No cross-reaction was observed with other similar viruses, indicating that the assay is highly specific for PKoV. To investigate the prevalence of PKoV in symptomatic pigs in Sichuan province, the newly developed method was used to detect PKoV in a panel of clinical specimens, yielding a positive rate of 86.7% (144/166) in piglets. The results showed that the RT-LAMP assay is highly feasible in clinical settings. The data confirm that the RT-LAMP assay is rapid, simple and cost-effective and is particularly suitable for simple diagnosis of PKoV both in the field and in the laboratory.
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Affiliation(s)
- Xinqiong Li
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Yuanchen Zhou
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Hongwei Ji
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Zhiwen Xu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China; Key Laboratory of Animal Disease and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
| | - Ling Zhu
- Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China; Key Laboratory of Animal Disease and Human Health, College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, China.
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Li JY, Wei QW, Liu Y, Tan XQ, Zhang WN, Wu JY, Charimbu MK, Hu BS, Cheng ZB, Yu C, Tao XR. One-step reverse transcription loop-mediated isothermal amplification for the rapid detection of cucumber green mottle mosaic virus. J Virol Methods 2013; 193:583-8. [PMID: 23933076 DOI: 10.1016/j.jviromet.2013.07.059] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/20/2013] [Accepted: 07/22/2013] [Indexed: 10/26/2022]
Abstract
Cucumber green mottle mosaic virus (CGMMV) has caused serious damage to Cucurbitaceae crops worldwide. The virus is considered one of the most serious Cucurbitaceae quarantine causes in many countries. In this study, a highly efficient and practical one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for the detection of CGMMV. The total RNA or crude RNA extracted from watermelon plants or seeds could be detected easily by this RT-LAMP assay. The RT-LAMP assay was conducted in isothermal (63°C) conditions within 1h. The amplified products of CGMMV could be detected as ladder-like bands using agarose gel electrophoresis or visualized in-tube under UV light with the addition of a fluorescent dye. The RT-LAMP amplification was specific to CGMMV, as no cross-reaction was observed with other viruses. The RT-LAMP assay was 100-fold more sensitive than that of reverse-transcription polymerase chain reaction (RT-PCR). This is the first report of the application of the RT-LAMP assay to detect CGMMV. The sensitive, specific and rapid RT-LAMP assay developed in this study can be applied widely in laboratories, the field and quarantine surveillance of CGMMV.
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Affiliation(s)
- Jin-yu Li
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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