Development of a LAMP assay with a portable device for real-time detection of begomoviruses under field conditions

Wilisiani, Fariha; Tomiyama, Aika; Katoh, Hiroshi; Hartono, Slamet; Neriya, Yutaro; Nishigawa, Hisashi; Natsuaki, Tomohide

doi:10.1016/j.jviromet.2018.10.005

Cited by 46 publications

(33 citation statements)

References 24 publications

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“…TYLCKaV sequences from Vietnam and Cambodia formed a different clade from those found in Thailand, Laos, China (Yunnan province), and Indonesia, indicating movement toward differentiation in Southeast Asia. Wilisiani et al (2019) detected PepYLCIV, TYLCKaV, and ToLCNDV from Solanaceae and Cucurbitaceae crops with a loop-mediated isothermal amplification assay. In the present study conducted in Aceh province, Indonesia, in addition to the ones mentioned before, PepYLCAV, SLCCNV, and AYVV were the predominant begomoviruses for horticultural crops.…”

Section: Resultsmentioning

confidence: 99%

Molecular Characterization of Begomoviruses Associated with Yellow Leaf Curl Disease in Solanaceae and Cucurbitaceae Crops from Northern Sumatra, Indonesia

et al. 2020

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Begomoviruses, transmitted by whiteflies (Bemisia tabaci), have emerged as serious constraints to the cultivation of a wide variety of vegetable crops worldwide. Leaf samples from Solanaceae (tomato, tobacco, and eggplant) and Cucurbitaceae (cucumber and squash) plants exhibiting typical begomoviral yellowing and/or curling symptoms were collected in Northern Sumatra, Aceh province, Indonesia. Rolling circle amplification was conducted using DNA isolated from cucumber, squash, eggplant, and tobacco, and the fulllength sequences of the begomoviruses were evaluated. The following viruses were isolated: bipartite begomoviruses Tomato leaf curl New Delhi virus (ToLCNDV), Squash leaf curl China virus (SLCCNV), Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV), and a monopartite begomovirus Ageratum yellow vein virus (AYVV). Begomovirus diagnosis was conducted by PCR using begomovirus species-specific primers for Pepper yellow leaf curl Indonesia virus (PepYLCIV), Pepper yellow leaf curl Aceh virus (PepYLCAV), ToLCNDV, SLCCNV, TYLCKaV, and AYVV, which are the predominant begomoviruses. The primary begomovirus species for each plant were as follows: PepYLCAV for tomato, AYVV for tobacco, TYLCKaV for eggplant, ToLCNDV for cucumber, and SLCCNV for squash. This study provides valuable information for breeding begomovirus-resistant cultivars as horticultural crops.

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Section: Resultsmentioning

confidence: 99%

Molecular Characterization of Begomoviruses Associated with Yellow Leaf Curl Disease in Solanaceae and Cucurbitaceae Crops from Northern Sumatra, Indonesia

et al. 2020

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“…RPA and LAMP isothermal amplification can be performed with crude plant extracts in portable hot blocks and results can be displayed with a portable fluorescence reader or a lateral flow strip so the whole process can take about 45 min. (Zhang et al, 2014;Wilisiani et al, 2019). Oxford Nanopore Technologies has developed MinION, a portable nanopore sequencing device, that can be used for the detection of plant viruses in the field (Boykin et al, 2018;Filloux et al, 2018;Shaffer, 2019), but it is still too expensive for most routine uses.…”

Section: Feasibility and Designabilitymentioning

confidence: 99%

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

2020

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Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable.

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“…Thus, several protocols in plant pathology were developed, where crude plant saps were used as template. This implementation accelerated the time for the diagnosis, avoiding any previous step for samples preparation and DNA or RNA purification [26,[34][35][36][37][38][39]. In that way, diagnosis time was speeded up for 2-3 h, which was necessary to complete the extraction of DNA/RNA of target organism.…”

Section: Lamp Accelerationmentioning

confidence: 99%

“…Recently, the development of LAMP portable devices has allowed a 'real-time' detection pathogen directly on-field [39,164], facilitating their diagnosis during the routine surveys or in sanitary selection or eradication programs.…”

Section: Lamp Application In Plant Virologymentioning

confidence: 99%

“…This approach permits the real-time detection of 1-4 target sequences in a single LAMP reaction tube, using a standard real-time fluorimeter, with standard LAMP primers that contain a quencher-fluorophore duplex region, which, upon strand separation, results in a gain of fluorescent signal [174]. Multiplex LAMP assays are now available for simultaneous detection of plant viruses [28,39].…”

Section: Multiplex Lamp (Mlamp)mentioning

confidence: 99%

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Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology

Panno

Matić

Tiberini³

et al. 2020

Plants

156

111

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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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Development of a LAMP assay with a portable device for real-time detection of begomoviruses under field conditions

Cited by 46 publications

References 24 publications

Molecular Characterization of Begomoviruses Associated with Yellow Leaf Curl Disease in <i>Solanaceae</i> and <i>Cucurbitaceae</i> Crops from Northern Sumatra, Indonesia

Molecular Characterization of Begomoviruses Associated with Yellow Leaf Curl Disease in <i>Solanaceae</i> and <i>Cucurbitaceae</i> Crops from Northern Sumatra, Indonesia

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology

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