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Zhao Z, Tian Y, Xu C, Xing Y, Yang L, Qian G, Hua X, Gong W, Hu B, Wang L. A Monoclonal Antibody-Based Immunochromatographic Test Strip and Its Application in the Rapid Detection of Cucumber Green Mottle Mosaic Virus. BIOSENSORS 2023; 13:199. [PMID: 36831965 PMCID: PMC9953337 DOI: 10.3390/bios13020199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Two specific monoclonal antibodies (mAbs) were screened, and an immunochromatographic strip (ICS) test for rapid and specific detection of cucumber green mottle mosaic virus (CGMMV) was developed. The coat protein of CGMMV was heterologously expressed as an immunogen, and specific capture mAb 2C9 and the detection mAb 4D4 were screened by an uncompetitive immunoassay. The test and control lines on the nitrocellulose membrane were coated with the purified 2C9 and a goat anti-mouse IgG, respectively, and a nanogold probe combined with 4D4 was applied to the conjugate pad. Using these mAbs, a rapid and sensitive ICS was developed. Within the sandwich mode of 2C9-CGMMV-4D4, the test line showed a corresponding positive relationship with CGMMV in infected samples. The ICS test had a detection limit of 1:5000 (w/v) for CGMMV in samples and was specific for CGMMV, with no observed cross-reaction with TMV or CMV.
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Affiliation(s)
- Zichen Zhao
- Department of Phytopathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanli Tian
- Department of Phytopathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Chang Xu
- Department of Phytopathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanfei Xing
- Department of Phytopathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Lili Yang
- Department of Phytopathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Guoliang Qian
- Department of Phytopathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiude Hua
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Weirong Gong
- Plant Protection and Quarantine Station of Jiangsu Province, Nanjing 210036, China
| | - Baishi Hu
- Department of Phytopathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Limin Wang
- Department of Phytopathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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2
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Rapid Quantification of Infectious Cucumber green mottle mosaic virus in Watermelon Tissues by PMA Coupled with RT-qPCR. Viruses 2022; 14:v14092046. [PMID: 36146852 PMCID: PMC9506375 DOI: 10.3390/v14092046] [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: 08/29/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) belongs to the Tobamovirus genus and is an important quarantine virus of cucurbit crops. Seedborne transmission is one of the principal modes for CGMMV spread, and effective early detection is helpful to prevent the occurrence of the disease. Quantitative real-time reverse-transcription PCR (RT-qPCR) is a sensitive and rapid method for detecting CGMMV nucleic acids, but it cannot distinguish between infectious and noninfectious viruses. In the present work, a propidium monoazide (PMA) assisted RT-qPCR method (PMA-RT-qPCR) was developed to rapidly distinguish infectious and inactive CGMMV. PMA is a photoactive dye that can selectively react with viral RNA released or inside inactive CGMMV virions but not viral RNA inside active virions. The formation of PMA-RNA conjugates prevents PCR amplification, leaving only infectious virions to be amplified. The primer pair cp3-1F/cp3-1R was designed based on the coat protein (cp) gene for specific amplification of CGMMV RNA by RT-qPCR. The detection limit of the RT-qPCR assay was 1.57 × 102 copies·μL−1. PMA at 120 μmol·L−1 was suitable for the selective quantification of infectious CGMMV virions. Under optimal conditions, RT-qPCR detection of heat-inactivated CGMMV resulted in Ct value differences larger than 16 between PMA-treated and non-PMA-treated groups, while Ct differences less than 0.23 were observed in the detection of infectious CGMMV. For naturally contaminated watermelon leaf, fruit and seedlot samples, infectious CGMMV were quantified in 13 out of the 22 samples, with infestation levels of 102~105 copies·g−1. Application of this assay enabled the selective detection of infectious CGMMV and facilitated the monitoring of the viral pathogen in watermelon seeds and tissues, which could be useful for avoiding the potential risks of primary inoculum sources.
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Pitman TL, Vu S, Tian T, Posis K, Falk BW. Genome and Phylogenetic Analysis of Cucumber Green Mottle Mosaic Virus Global Isolates and Validation of a Highly Sensitive RT-qPCR Assay. PLANT DISEASE 2022; 106:1713-1722. [PMID: 35134301 DOI: 10.1094/pdis-10-21-2263-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The last two decades have seen exponential growth in the international movement of seeds for annual food crops, from a gross U.S. import value of $349 million in 1999 to $1.05 billion in 2019. This has led to the proportionate growth of seedborne pathogens dispersed with seed stocks. One such viral pathogen is cucumber green mottle mosaic virus (CGMMV), a tobamovirus that infects cucurbit crops such as melon, watermelon, cucumber, pumpkin, and squash. The first CGMMV introduction to California occurred in 2013, with subsequent annual outbreaks or detections since then. Here, we describe the use of next-generation sequencing to characterize the full genomes of 25 CGMMV isolates collected between 2013 and 2020 in California, either from CGMMV field detections or seed lots identified as CGMMV positive. We sequenced an additional 31 CGMMV isolates collected in Europe, Israel, and southeast Asia that were provided by industry collaborators. We also performed an in silico nucleotide database search in GenBank for full genome CGMMV sequences to include in all in silico analyses. Based on conserved regions within the coat protein gene, we then developed a quantitative reverse-transcription PCR assay for the sensitive and specific detection of CGMMV in seed and plant samples. Finally, based on our sequence and phylogenetic analysis, our data support that CGMMV has been introduced multiple times into California.
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Affiliation(s)
- T L Pitman
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - S Vu
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - T Tian
- California Department of Food and Agriculture, Sacramento, CA 95832
| | - K Posis
- California Department of Food and Agriculture, Sacramento, CA 95832
| | - B W Falk
- Department of Plant Pathology, University of California, Davis, CA 95616
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Gawande SP, Raghavendra KP, Monga D, Nagrale DT, Prabhulinga T, Hiremani N, Meshram M, Kranthi S, Gokte-Narkhedkar N, Waghmare VN. Development of Loop Mediated Isothermal Amplification (LAMP): A new tool for rapid diagnosis of cotton leaf curl viral disease. J Virol Methods 2022; 306:114541. [PMID: 35568082 DOI: 10.1016/j.jviromet.2022.114541] [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: 12/17/2020] [Revised: 05/05/2022] [Accepted: 05/08/2022] [Indexed: 10/18/2022]
Abstract
Cotton leaf curl disease (CLCuD) ranks top among all endemic diseases transmitted by whitefly (Bemisia tabaci) affecting cotton (Gossypium hirsutum) causing severe economic losses to the cotton growers in the Indian subcontinent. For its effective management, robust tools for detection are a prerequisite and it is important to diagnose the virus titre in early stage of infection in plants as well as in the disease transmitting vector. Considering the limitations in current PCR-based techniques we have standardized rapid and sensitive Loop Mediated Isothermal Amplification (LAMP) protocol for the diagnosis of cotton leaf curl virus (CLCuV) in cotton leaves and in its transmitting vector whitefly. Perhaps, this is the first report of use of LAMP tool for rapid diagnosis of CLCuV in cotton and its transmitting vector the whitefly. Further, the colorimetric detection for diagnostic simplicity of amplified LAMP product by using different dyes lead to enhanced applicability of this technique in the field of disease diagnostics. The merit of present study is that the diagnostic failure of PCR and LAMP due to low virus titre in the infected leaf has been circumvented through the combination of rolling circle amplification (RCA) with LAMP. Thus RCA-LAMP can be an option for ultra-sensitive detection of samples with low virus titre. The potential applications of this advanced diagnostic tool in laboratory research on diagnosis of CLCuV, an important viral pathogen of cotton have been discussed.
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Affiliation(s)
- S P Gawande
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India.
| | - K P Raghavendra
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - D Monga
- ICAR- Central Institute for Cotton Research Regional Station (ICAR-CICR RS), Sirsa -125055, India
| | - D T Nagrale
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - T Prabhulinga
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - N Hiremani
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - M Meshram
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
| | - Sandhya Kranthi
- Project Consultant, International Cotton Advisory Committee (ICAC), Washington DC, USA
| | | | - V N Waghmare
- ICAR-Central Institute for Cotton Research (ICAR-CICR), Nagpur-440010, India
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5
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Zhao W, Wu S, Du L, Li T, Cheng Z, Zhou Y, Ji Y. Development of a reverse-transcription loop-mediated isothermal amplification assay for the detection of Tobacco mild green mosaic virus (TMGMV). J Virol Methods 2021; 298:114277. [PMID: 34492235 DOI: 10.1016/j.jviromet.2021.114277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 08/02/2021] [Accepted: 09/02/2021] [Indexed: 11/22/2022]
Abstract
Tobacco mild green mosaic virus (TMGMV), a member species of the genus Tobamovirus, infects pepper (Capsicum annuum) and a number of other economically important species in the Solanaceae family. TMGMV infections had seriously impacted pepper production worldwide, including China. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect TMGMV in pepper field samples and seed. This assay was based on four primers that matched to six sequences in the C-terminal region of the TMGMV genome. RT-LAMP assay could detect the presence of the virus in 3.0 × 10-7 µg of total RNA extract from pepper leaves, which was ten times more sensitive than the corresponding reverse-transcription polymerase chain reaction (RT-PCR) assay. This method specifically detected TMGMV but not the closely related species of the same genus Pepper mild mottle virus, Cucumber green mottle mosaic virus and Tomato mosaic virus. In addition, the use of SYBR Green I facilitated the detection of the TMGMV RT-LAMP products by the naked eye. These results indicated that the RT-LAMP assay was a simple, sensitive, specific and affordable diagnostic tool that has the potential to detect and monitor TMGMV infection in field samples.
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Affiliation(s)
- Wenhao Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Shuhua Wu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Linlin Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Tingfang Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Zhaobang Cheng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China
| | - Yinghua Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences/Key Lab of Food Quality and Safety of Jiangsu Province - State Key Laboratory Breeding Base, Nanjing 210014, China.
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6
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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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7
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Kokane AD, Kokane SB, Warghane AJ, Gubyad MG, Sharma AK, Reddy MK, Ghosh DK. A Rapid and Sensitive Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for the Detection of Indian Citrus Ringspot Virus. PLANT DISEASE 2021; 105:1346-1355. [PMID: 32990524 DOI: 10.1094/pdis-06-20-1349-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Indian citrus ringspot virus (ICRSV) is a devastating pathogen that has a particularly deleterious effect on the 'Kinnow mandarin', a commercial citrus crop cultivated in the northwest of India. ICRSV belongs to the Mandarivirus genus within the family of Alphaflexiviridae and has a positive sense single-stranded RNA (ssRNA) genome consisting of six open reading frames (ORFs). Severe cases of ICRSV result in a significant reduction in both the yield and quality of crops. Consequently, there is an urgent need to develop methods to detect ICRSV in an accurate and timely manner. Current methods involve a two-step reverse transcription polymerase chain reaction (RT-PCR) that is time consuming. Here, we describe a novel, one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the sensitive and rapid detection of ICRSV. To standardize the RT-LAMP assay, four different primers were designed and tested to target the coat protein gene of ICRSV. Amplification results were visualized by a color change after addition of SYBR Green I. The standardized RT-LAMP assay was highly specific and successfully detected all 35 ICRSV isolates tested from the Punjab and Haryana states of India. Furthermore, there was no cross-reaction with 17 isolates of five other citrus pathogens that are common in India. The ICRSV RT-LAMP assay developed in the present study is a simple, rapid, sensitive, specific technique. Moreover, the assay consists of only a single step and is more cost effective than existing methods. This is the first application of RT-LAMP for the detection of ICRSV. Our RT-LAMP assay is a powerful tool for the detection of ICRSV and will be particularly useful for large-scale indexing of field samples in diagnostic laboratories, in nurseries, and for quarantine applications.
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Affiliation(s)
- Amol D Kokane
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Sunil B Kokane
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Ashish J Warghane
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Mrugendra G Gubyad
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology, Roorkee-247 667, Uttarakhand, India
| | - M Krishna Reddy
- ICAR-Indian Institute of Horticultural Research, Bangalore-560 089, Karnataka, India
| | - Dilip Kumar Ghosh
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, 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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9
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Qiao N, Dai H, Liu J, Zhu X, Li J, Zhang D, Liu Y. Detection of melon necrotic spot virus by one-step reverse transcription loop-mediated isothermal amplification assay. PLoS One 2020; 15:e0230023. [PMID: 32134962 PMCID: PMC7058275 DOI: 10.1371/journal.pone.0230023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Melon necrotic spot virus (MNSV) can cause significant economic losses due to decreased quality in cucurbit crops. The current study is the first to use reverse transcription loop-mediated isothermal amplification (RT-LAMP) for detection of MNSV. A set of four LAMP primers was designed based on the coat protein gene sequence of MNSV, and a RT-LAMP reaction was successfully performed for 1 h at 62°C. The results of RT-LAMP showed high specificity for MNSV and no cross-reaction with other viruses. Compared to traditional reverse transcription-PCR (RT-PCR), the RT-LAMP assay was 103-fold more sensitive in detecting MNSV. Due to its sensitivity, speed and visual assessment, RT-LAMP is appropriate for detecting MNSV in the laboratory.
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Affiliation(s)
- Ning Qiao
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Huijie Dai
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Jie Liu
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Xiaoping Zhu
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
- * E-mail:
| | - Jintang Li
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Dezhen Zhang
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Yongguang Liu
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
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10
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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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11
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Bi X, Li X, Yu H, An M, Li R, Xia Z, Wu Y. Development of a multiplex RT-PCR assay for simultaneous detection of Cucumber green mottle mosaic virus and Acidovorax citrulli in watermelon. PeerJ 2019; 7:e7539. [PMID: 31497401 PMCID: PMC6708580 DOI: 10.7717/peerj.7539] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022] Open
Abstract
Watermelon (Citrullus lanatus Thunb.) is considered as a popular and nutritious fruit crop worldwide. Watermelon blood flesh disease caused by Cucumber green mottle mosaic virus (CGMMV) and bacterial fruit blotch caused by Acidovorax citrulli, are two major quarantine diseases of watermelon and result in considerable losses to global watermelon production. In this study, a multiplex reverse-transcription polymerase chain reaction (RT-PCR) method was developed for simultaneous detection of CGMMV and A. citrulli in both watermelon leaves and seeds. Two pairs of specific primers were designed based on the conserved sequences of the genomic RNA of CGMMV and the internal transcribed spacer of A. citrulli, respectively. Transcriptional elongation factor-1α from watermelon was added as an internal reference gene to prevent false negatives. No cross-reactivity was detected with other viral or bacterial pathogens infecting watermelon. Moreover, the multiplex RT-PCR showed high sensitivity and could simultaneously detect CGMMV and A. citrulli as little as 102 copies of plasmid DNA. This method was successfully applied to test field-collected watermelon leaves and stored seeds of cucurbitaceous crops. These results suggested that the developed multiplex RT-PCR technique is a rapid, efficient, and sensitive method for simultaneous detection of CGMMV and A. citrulli, providing technical support for monitoring, predicting, and preventing these two quarantine diseases. To our knowledge, this is the first report on simultaneous detection of a virus and a bacterium by multiplex RT-PCR in watermelon.
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Affiliation(s)
- Xinyue Bi
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xiaodong Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
- General Station of Forest and Grassland Pest and Diseases Control, National Forestry and Grassland Administration, Shenyang, Liaoning, China
| | - Haibo Yu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Mengnan An
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Rui Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Zihao Xia
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
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12
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Gawande SP, K P R, Monga D, Nagrale DT, Kranthi S. Rapid detection of Tobacco streak virus (TSV) in cotton (Gossypium hirsutum) based on Reverse Transcription Loop Mediated Isothermal Amplification (RT-LAMP). J Virol Methods 2019; 270:21-25. [PMID: 31026558 DOI: 10.1016/j.jviromet.2019.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/06/2019] [Accepted: 04/20/2019] [Indexed: 12/01/2022]
Abstract
Tobacco Streak Virus (TSV) belongs to the genus Ilarvirus of the family Bromoviridae an emerging pathogen posing threat to the crop species worldwide. Identification of symptoms due to TSV infection by visual observation of plants often results in misdiagnosis as symptoms produced by this virus can match with those reflecting physiological and nutritional disorders affecting cotton. Development of diagnostic tools with rapidity will have immense role to play in detection and management of the emerging virus. The protocol for rapid diagnosis of TSV infected samples by using Reverse Transcription-Loop Mediated Isothermal Amplification (RT-LAMP) was optimised and this is the first report of its use for diagnosis of TSV on cotton and Soybean. The colorimetric detection for diagnostic simplicity of amplified RT-LAMP product by using different dyes lead to enhanced applicability of this technique. The RT-LAMP diagnostic tool can be utilized not only for laboratory research but also for quarantine and field diagnosis of this important emerging pathogen affecting cotton.
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Affiliation(s)
| | - Raghavendra K P
- Division of Crop Improvement, ICAR-Central Institute for Cotton Research (CICR), Nagpur, 440010, India
| | - Dilip Monga
- ICAR- Central Institute for Cotton Research (CICR), Regional Station, Sirsa, 125055, India
| | - Dipak T Nagrale
- Division of Crop Protection, ICAR-Central Institute for Cotton Research (CICR), Nagpur, 440010, India
| | - Sandhya Kranthi
- Division of Crop Protection, ICAR-Central Institute for Cotton Research (CICR), Nagpur, 440010, India
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13
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Sui X, Li R, Shamimuzzaman M, Wu Z, Ling KS. Understanding the Transmissibility of Cucumber Green Mottle Mosaic Virus in Watermelon Seeds and Seed Health Assays. PLANT DISEASE 2019; 103:1126-1131. [PMID: 30995423 DOI: 10.1094/pdis-10-18-1787-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cucumber green mottle mosaic virus (CGMMV), an emerging tobamovirus, has caused serious disease outbreaks to cucurbit crops in several countries, including the United States. Although CGMMV is seed-borne, the mechanism of its transmission from a contaminated seed to germinating seedling is still not fully understood, and the most suitable seed health assay method has not been well established. To evaluate the mechanism of seed transmissibility, using highly contaminated watermelon seeds collected from CGMMV-infected experimental plants, bioassays were conducted in a greenhouse through seedling grow-out and by mechanical inoculation. Through natural seedling grow-out, we did not observe seed transmission of CGMMV to germinating seedlings. However, efficient transmission of CGMMV was observed using bioassays on melon plants through mechanical inoculation of seed extract prepared from CGMMV-contaminated seeds. Understanding the seed-borne property and the ease of mechanical transmission of CGMMV from a contaminated seed to seedling is an important finding. In comparative evaluation of various laboratory techniques for seed health assays, we found that enzyme-linked immunosorbent assay and loop-mediated isothermal amplification were the most sensitive and reliable methods to detect CGMMV on cucurbit seeds. Because CGMMV is a seed-borne and highly contagious virus, a new infection might not result in a natural seedling grow-out; it could occur through mechanical transmission from contaminated seeds. Therefore, a sensitive seed health test is necessary to ensure CGMMV-free seed lots are used for planting.
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Affiliation(s)
- Xuelian Sui
- 1 State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China; and
- 2 U.S. Vegetable Laboratory, USDA-Agricultural Research Service, Charleston, SC, U.S.A
| | - Rugang Li
- 2 U.S. Vegetable Laboratory, USDA-Agricultural Research Service, Charleston, SC, U.S.A
| | - Md Shamimuzzaman
- 2 U.S. Vegetable Laboratory, USDA-Agricultural Research Service, Charleston, SC, U.S.A
| | - Zujian Wu
- 1 State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China; and
| | - Kai-Shu Ling
- 2 U.S. Vegetable Laboratory, USDA-Agricultural Research Service, Charleston, SC, U.S.A
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14
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Congdon BS, Kehoe MA, Filardo FF, Coutts BA. In-field capable loop-mediated isothermal amplification detection of Turnip yellows virus in plants and its principal aphid vector Myzus persicae. J Virol Methods 2018; 265:15-21. [PMID: 30578895 DOI: 10.1016/j.jviromet.2018.12.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 11/24/2022]
Abstract
Widespread Turnip yellows virus (TuYV) infection causes severe seed yield and quality losses in rapeseed (Brassica napus) crops grown in broadacre agricultural systems worldwide. Current TuYV detection protocols are expensive and time consuming, and can have poor specificity and sensitivity. Typically, they are used as a diagnostic tool to test already symptomatic plants, limiting their practical value to reactive disease management. To improve diagnostic services so that they provide earlier, cheaper, faster, more specific and sensitive TuYV detection, novel and innovative protocols that utilise new technology are required. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect TuYV in crude and total RNA extractions of leaf material and its principal aphid vector Myzus persicae. The assay was based on a set of six primers, highly sensitive and specific to TuYV, derived from a TuYV isolate originating from the south-west Australian grainbelt. TuYV was readily detected in 1 in 100 dilutions of (i) infected to uninfected leaf material, and (ii) viruliferous to non-viruliferous M. persicae. Furthermore, detection was successful in a majority of aphids stored for at least 8 weeks in various trapping and storage substances, including 30% ethylene glycol, sticky trap glue and 70% ethanol. This RT-LAMP assay protocol enables quicker and cheaper diagnosis for TuYV than currently adopted laboratory-based diagnostic techniques. Ultimately, it has the potential for earlier in-field TuYV detection in combination with aphid trapping surveillance programs.
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Affiliation(s)
- B S Congdon
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia.
| | - M A Kehoe
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia
| | - F F Filardo
- Ecosciences Precinct, Queensland Department of Agriculture and Fisheries, GPO Box 46, Brisbane, Queensland, 4001, Australia
| | - B A Coutts
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia
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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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Wang L, Liu Z, Xia X, Yang C, Huang J, Wan S. Colorimetric detection of Cucumber green mottle mosaic virus using unmodified gold nanoparticles as colorimetric probes. J Virol Methods 2017; 243:113-119. [DOI: 10.1016/j.jviromet.2017.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 01/04/2017] [Accepted: 01/15/2017] [Indexed: 02/02/2023]
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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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Itonaga M, Matsuzaki I, Warigaya K, Tamura T, Shimizu Y, Fujimoto M, Kojima F, Ichinose M, Murata SI. Novel Methodology for Rapid Detection of KRAS Mutation Using PNA-LNA Mediated Loop-Mediated Isothermal Amplification. PLoS One 2016; 11:e0151654. [PMID: 26999437 PMCID: PMC4801409 DOI: 10.1371/journal.pone.0151654] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/02/2016] [Indexed: 12/20/2022] Open
Abstract
Detecting point mutation of human cancer cells quickly and accurately is gaining in importance for pathological diagnosis and choice of therapeutic approach. In the present study, we present novel methodology, peptide nucleic acid—locked nucleic acid mediated loop-mediated isothermal amplification (PNA-LNA mediated LAMP), for rapid detection of KRAS mutation using advantages of both artificial DNA and LAMP. PNA-LNA mediated LAMP reactions occurred under isothermal temperature conditions of with 4 primary primers set for the target regions on the KRAS gene, clamping PNA probe that was complimentary to the wild type sequence and LNA primers complementary to the mutated sequences. PNA-LNA mediated LAMP was applied for cDNA from 4 kinds of pancreatic carcinoma cell lines with or without KRAS point mutation. The amplified DNA products were verified by naked-eye as well as a real-time PCR equipment. By PNA-LNA mediated LAMP, amplification of wild type KRAS DNA was blocked by clamping PNA probe, whereas, mutant type KRAS DNA was significantly amplified within 50 min. Mutant alleles could be detected in samples which diluted until 0.1% of mutant-to-wild type ratio. On the other hand, mutant alleles could be reproducibly with a mutant-to-wild type ratio of 30% by direct sequencing and of 1% by PNA-clamping PCR. The limit of detection (LOD) of PNA-LNA mediated LAMP was much lower than the other conventional methods. Competition of LNA clamping primers complementary to two different subtypes (G12D and G12V) of mutant KRAS gene indicated different amplification time depend on subtypes of mutant cDNA. PNA-LNA mediated LAMP is a simple, rapid, specific and sensitive methodology for the detection of KRAS mutation.
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Affiliation(s)
- Masahiro Itonaga
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
- Second Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Ibu Matsuzaki
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Kenji Warigaya
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Takaaki Tamura
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Yuki Shimizu
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Masakazu Fujimoto
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Fumiyoshi Kojima
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Masao Ichinose
- Second Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Shin-ichi Murata
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
- * E-mail:
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19
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Pan L, Li J, Xia W, Zhang D, Dong L. An effective method, composed of LAMP and dCAPS, to detect different mutations in fenoxaprop-P-ethyl-resistant American sloughgrass (Beckmannia syzigachne Steud.) populations. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2015; 117:1-8. [PMID: 25619905 DOI: 10.1016/j.pestbp.2014.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 05/20/2023]
Abstract
The decreased susceptibility of Beckmannia syzigachne to fenoxaprop-P-ethyl is due to the reliance on it to control grass weeds since the 1990s. Loop-mediated isothermal amplification (LAMP), which is a proven simple, rapid, specific, sensitive and inexpensive assay method, has been used to detect the I1781L mutation in B. syzigachne. In the present study, four sets of primers detected four mutations in B. syzigachne, W2027C, I2041A, D2078G and G2096A, using the LAMP method. Additionally, five newly derived cleaved amplified polymorphic sequence (dCAPS) markers were developed to detect five different mutations. With a method composed of LAMP and dCAPS, 19 fenoxaprop-P-ethyl-resistant B. syzigachne populations collected in 2013 were studied. An effective method, composed of LAMP and dCAPS, to detect five mutations, I1781L, W2027C, I2041A, D2078G and G2096A, in B. syzigachne populations was developed. With this method, a B. syzigachne population resistant to fenoxaprop-P-ethyl can be studied to confirm its constitution. And we determined that the resistance level might be relevant to the mutation type and mutation frequency. The type of mutation and its frequency in fenoxaprop-P-ethyl-resistant B. syzigachne populations can be confirmed to provide appropriate herbicide management.
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Affiliation(s)
- Lang Pan
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
| | - Jun Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
| | - Wenwen Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
| | - Di Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China
| | - Liyao Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing 210095, China.
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20
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Pan L, Li J, Zhang WN, Dong L. Detection of the I1781L mutation in fenoxaprop-p-ethyl-resistant American sloughgrass (Beckmannia syzigachne Steud.), based on the loop-mediated isothermal amplification method. PEST MANAGEMENT SCIENCE 2015; 71:123-30. [PMID: 24644047 DOI: 10.1002/ps.3777] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The increasing use of fenoxaprop-p-ethyl has resulted in evolved resistance in American sloughgrass (Beckmannia syzigachne Steud.). Target-site-based resistance to acetyl-CoA carboxylase (ACCase) inhibitors in B. syzigachne occurs owing to an isoleucine-to-leucine substitution at residue 1781 (I1781L) of the ACCase enzyme. A rapid detection method is needed to identify the resistance-conferring substitution. RESULTS Four populations of B. syzigachne that were resistant to fenoxaprop-p-ethyl and contained the I1781L substitution were identified. Conventional PCR and derived cleaved amplified polymorphic sequence (dCAPS) methods were used to detect the mutation. Additionally, a rapid nucleic acid detection method, loop-mediated isothermal amplification (LAMP), was successfully developed and used to detect the genetic mutation underlying the I1781L substitution in the B. syzigachne ACCase enzyme. CONCLUSION This report is the first to describe the application of a LAMP assay for mutation detection in herbicide-resistant weeds. The assay does not require specialised equipment: only a standard laboratory bath is needed. This technique could be employed for detecting the I1781L substitution in B. syzigachne plants and seeds.
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Affiliation(s)
- Lang Pan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, China
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21
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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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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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