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Arutselvan R, Makeshkumar T. Single-tube colorimetric loop-mediated isothermal amplification (LAMP) assay for high-sensitivity detection of SLCMV in cassava from southern India. Microb Pathog 2024; 192:106718. [PMID: 38815777 DOI: 10.1016/j.micpath.2024.106718] [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: 02/27/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/01/2024]
Abstract
Sri Lankan cassava mosaic virus (SLCMV) is a major cause for mosaic infections in cassava leaves, resulting in significant economic losses in southern India. SLCMV leads to growth retardation, leaf curl, and chlorosis in the host, with rapid transmission through whitefly insect vectors. Detecting SLCMV promptly is crucial, and the study introduces a novel and efficient colorimetric Loop-mediated isothermal amplification (LAMP) assay for successful detection in 60 min. Three primer sets were designed to target the conserved region of the SLCMV genome, specifically the coat protein gene, making the assay highly specific. The LAMP assay offers rapid and sensitive detection, completing within 60 min in a temperature-controlled water bath or thermal cycler. Compared to PCR techniques, it demonstrates 100 times superior sensitivity. The visual inspection of LAMP tube results using a nucleic acid dye and observing ladder-like pattern bands in a 2 % agarose gel confirms the presence of SLCMV. The assay is specific to SLCMV, showing no false positives or contaminations when tested against other virus. The standardized SLCMV LAMP assay proves technically efficient, providing a rapid, specific, simple, and low-cost solution, streamlining the detection and management of SLCMV.
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Affiliation(s)
- R Arutselvan
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - T Makeshkumar
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India.
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Xu T, Yang X, Feng X, Luo H, Luo C, Jia MA, Lei L. Sensitive and Visual Detection of Brassica Yellows Virus Using Reverse Transcription Loop-Mediated Isothermal Amplification-Coupled CRISPR-Cas12 Assay. PHYTOPATHOLOGY 2024; 114:474-483. [PMID: 37589413 DOI: 10.1094/phyto-06-23-0195-r] [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: 08/18/2023]
Abstract
Brassica yellows virus (BrYV) is an economically important virus on cruciferous species. In this study, a one-pot reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system was developed for the detection of BrYV. The limit of detection of this method reached 32.8 copies of the BrYV ORF5, which is 100-fold more sensitive than the RT-LAMP method. Moreover, there was no cross-reactivity with other rapeseed-infecting RNA viruses or poleroviruses. We dried the CRISPR/Cas12a reagent in a trehalose and pullulan mixture to retain its efficacy at the RT-LAMP temperature of 63°C in order to allow portable BrYV detection in a water bath. The entire process can be performed in about 1 h, and a positive result can be rapidly and conveniently detected using a handheld UV lamp. In the field, the RT-LAMP-CRISPR/Cas12a assay was accurate and had higher sensitivity than RT-LAMP and reverse transcription-polymerase chain reaction assays. The novel RT-LAMP-CRISPR/Cas12a assay allows convenient, portable, rapid, low-cost, highly sensitive, and specific detection of BrYV and has great potential for on-site monitoring of BrYV.
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Affiliation(s)
- Tengzhi Xu
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xiaolan Yang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xia Feng
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Hao Luo
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Chun Luo
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Meng-Ao Jia
- Guizhou Academy of Tobacco Sciences, Guiyang, Guizhou 550001, China
| | - Lei Lei
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China
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Krishnan N, Kumari S, Kumar R, Pandey KK, Singh J. Loop-mediated isothermal amplification assay for quicker detection of tomato leaf curl Joydebpur virus infection in chilli. J Virol Methods 2022; 302:114474. [PMID: 35077721 DOI: 10.1016/j.jviromet.2022.114474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 12/21/2021] [Accepted: 01/20/2022] [Indexed: 11/26/2022]
Abstract
Chilli leaf curl disease caused by whitefly transmitted begomoviruses is an important constraint to chilli (Capsicum anuum L.) cultivation in India. Tomato leaf curl Joydebpur virus (ToLCJoV) was characterized and identified as incitant of leaf curl disease through rolling circle amplification (RCA) and PCR assay from the symptomatic samples collected from Uttar Pradesh, India. Although PCR assay provides the gold standard in diagnostics, this method consumes more time and requires convenient portable instruments. Therefore, a loop-mediated isothermal amplification (LAMP) assay was developed for the detection of ToLCJoV by targeting the AC1 and AC2 region. Detection has been achieved through a laddered pattern of amplification in agarose gel electrophoresis. The assay has detected ToLCJoV in a total DNA concentration of 1 × 10-1 ng indicating 200-fold higher sensitivity than that of the PCR. Further, the replacement of total DNA with leaf extracts using the grinding buffer and GES buffer coupled with LAMP assay also detected the presence of ToLCJoV in the infected chilli samples. With this assay, ToLCJoV can be detected in less than 2 h without DNA extraction. Besides, this assay will be highly useful in discriminating the leaf curl disease etiology by ToLCJoV from other begomoviruses and insects (thrips and mites). To the best of our knowledge, this is the first report of a LAMP assay for the detection of ToLCJoV.
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Affiliation(s)
- Nagendran Krishnan
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India.
| | - Shweta Kumari
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
| | - Rajesh Kumar
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
| | | | - Jagdish Singh
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
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Rafiq A, Ali WR, Asif M, Ahmed N, Khan WS, Mansoor S, Bajwa SZ, Amin I. Development of a LAMP assay using a portable device for the real-time detection of cotton leaf curl disease in field conditions. Biol Methods Protoc 2021; 6:bpab010. [PMID: 34084942 PMCID: PMC8164779 DOI: 10.1093/biomethods/bpab010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022] Open
Abstract
Cotton production is seriously affected by the prevalent cotton leaf curl disease (CLCuD) that originated from Nigeria (Africa) to various parts of Asia including Pakistan, India, China and Philippines. Due to CLCuD, Pakistan suffers heavy losses approximately 2 billion USD per annum. Numerous reports showed that CLCuD is associated with multiple species of begomoviruses, alphasatellites and a single species of betasatellite, that is ‘Cotton leaf curl Multan betasatellite’ (CLCuMuB). The most prevalent form of CLCuD is the combination of ‘Cotton leaf curl Kokhran virus’-Burewala strain (CLCuKoV-Bur) and CLCuMuB. Thus, the availability of an in-field assay for the timely detection of CLCuD is important for the control and management of the disease. In this study, a robust method using the loop-mediated isothermal amplification (LAMP) assay was developed for the detection of CLCuD. Multiple sets of six primers were designed based on the conserved regions of CLCuKoV-Bur and CLCuMuB-βC1 genes. The results showed that the primer set targeting the CLCuMuB-βC1 gene performed best when the LAMP assay was performed at 58°C using 100 ng of total plant tissue DNA as a template in a 25 µl reaction volume. The limit of detection for the assay was as low as 22 copies of total purified DNA template per reaction. This assay was further adapted to perform as a colorimetric and real-time LAMP assay which proved to be advantageously applied for the rapid and early point-of-care detection of CLCuD in the field. Application of the assay could help to prevent the huge economic losses caused by the disease and contribute to the socio-economic development of underdeveloped countries.
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Affiliation(s)
- Amna Rafiq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 44000, Pakistan
| | - Waqas Rafique Ali
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Nasim Ahmed
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 44000, Pakistan
| | - Waheed S Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Sadia Zafar Bajwa
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
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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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Development of a LAMP assay with a portable device for real-time detection of begomoviruses under field conditions. J Virol Methods 2018; 265:71-76. [PMID: 30321578 DOI: 10.1016/j.jviromet.2018.10.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/07/2018] [Accepted: 10/12/2018] [Indexed: 02/02/2023]
Abstract
The emergence of begomovirus infection is one of the most important problems affecting production of a variety of vegetable crops worldwide. Infection by begomoviruses has been detected and spread rapidly on Cucurbitaceae and Solanaceae plants in Indonesia. A rapid and simple detection assay for begomoviruses under field conditions for routine sampling of plants is needed. Primers for a loop-mediated isothermal amplification (LAMP) assay were designed based on the sequences of three Indonesian begomoviruses, namely Tomato leaf curl New Delhi virus (ToLCNDV), Pepper yellow leaf curl Indonesia virus (PepYLCIV), and Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV), infecting Cucurbitaceae and Solanaceae plants. LAMP assays using a Genelyzer™ III portable fluorometer with a toothpick method successfully detected these begomoviruses in infected melon, pepper, and eggplant samples. LAMP assays conducted during a field survey for detection of the three begomoviruses on 104 fresh leaves indicated that most of the samples were positive; the findings were confirmed by PCR using universal primers of begomovirus as a common detection method. These results demonstrate that this simple and rapid LAMP assay using a fluorometer portable device may be used to achieve real-time detection of begomoviruses under field conditions.
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