Multiplex detection of three banana viruses by reverse transcription loop-mediated isothermal amplification (RT-LAMP)

Zhang, Jingxin; Borth, Wayne B.; Lin, Birun; Melzer, Michael; Shen, Huolin; Pu, Xiaoming; Sun, Dan; Nelson, Scot; Hu, John

doi:10.1007/s40858-018-0257-6

Cited by 20 publications

(14 citation statements)

References 41 publications

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“…Also, there is a limitation in the number of products of different sizes that can be resolved by electrophoresis or the number of fluorescent dyes that can be used ( Boonham et al., 2007 ). Multiplex LAMP has also been developed for the simultaneous detection of some plant viruses ( Zhang J. et al., 2018 ; Wilisiani et al., 2019 ). Molecular hybridization with cocktails of probes or polyprobes (probes linked in tandem) has been used to detect different viruses affecting a crop ( Sánchez-Navarro et al., 1999 ; Saade et al., 2000 ; Herranz et al., 2005 ; Aparicio et al., 2009 ; Minutillo et al., 2012 ), although further analyses are necessary to identify each virus.…”

Section: Detection Of Plant Virusesmentioning

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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Section: Detection Of Plant Virusesmentioning

confidence: 99%

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

2020

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“…This allows a threefold amplification of the target sequence at each half of the cycle [15,22]. Owing to the high displacement activity of the Bst DNA polymerase, a huge amount of DNA with a high molecular weight is rapidly generated [26][27][28]. This allows target DNA amplification until 10 9 copies in less than one hour.…”

Section: Cycling Amplification and Elongation Stepmentioning

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%

Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology

Panno

Matić

Tiberini³

et al. 2020

Plants

124

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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“…Thus, loop-mediated isothermal amplification is considered vastly specific and generates significantly more amplicons compared to polymerase chain reaction with less time period and excluding thermal cycler. This technique can further be multiplexed via implementing reverse transcriptase step for detecting ribonucleic acid targets (Zhang et al 2018 ). Moreover, loop-mediated isothermal amplification has minimum sensitivity towards inhibitors rather than polymerase chain reaction (Huang et al 2018 ).…”

Section: Technologies Available For Covid-19 Virus Detection and Idenmentioning

confidence: 99%

Detection and disinfection of COVID-19 virus in wastewater

et al. 2021

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The coronavirus disease 2019, COVID-19, caused by the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, appears as a major pandemic having adverse impact on public health and economic activities. Since viral replication in human enterocytes results in its faecal shedding, wastewater surveillance is an ideal, non-invasive, cost-effective and an early warning epidemiological approach to detect the genetic material of SARS-CoV-2. Here, we review techniques for the detection of SARS-CoV-2 in municipal wastewater, and disinfectants used to control viral spread. For detection, concentration of ribonucleic acid involves ultrafiltration, ultracentrifugation and polyethylene glycol precipitation. Identification is done by reverse transcriptase amplification, nucleic acid sequence-based amplification, helicase dependent amplification, loop-mediated isothermal amplification, recombinase polymerase amplification, high throughput screening and biosensor assays. Disinfectants include ultraviolet radiations, ozone, chlorine dioxide, hypochlorites and hydrogen peroxide. Wastewater surveillance data indicates viral presence within longer detection window, and provides transmission dynamics earlier than classical methods. This is particularly relevant for pre-symptomatic and asymptomatic COVID-19 cases.

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Multiplex detection of three banana viruses by reverse transcription loop-mediated isothermal amplification (RT-LAMP)

Cited by 20 publications

References 41 publications

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

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

Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology

Detection and disinfection of COVID-19 virus in wastewater

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