Development of a short oligonucleotide microarray for the detection and identification of multiple potyviruses

Wei, Ting; Pearson, M. N.; Blohm, Dietmar; Nölte, Manfred; Armstrong, Karen

doi:10.1016/j.jviromet.2009.07.024

Cited by 23 publications

(9 citation statements)

References 54 publications

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“…Sensitivity and specificity can be improved controlling the hybridization temperature and buffer composition (Boonham et al, 2007). Microarrays have been used to detect: i) viruses infecting a particular crop, such as tomato, cucurbits, potato and grapevine (Bystricka et al, 2003;Engel et al, 2010;Sip et al, 2010;Tiberini et al, 2010;Tiberini and Barba, 2012); ii) different viral species of a genus (Wei et al, 2009); and iii) isolates or variants of the same virus (Deyong et al, 2005;Pasquini et al, 2008). Microarrays have been improved to detect hundreds of plant viruses, including genus-specific oligoprobes (Zhang et al, 2010;Nicolaisen, 2011;Nam et al, 2014).…”

Section: Multiplexingmentioning

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: Multiplexingmentioning

confidence: 99%

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

2020

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“…Serological (ELISA) and molecular (PCR and RT-PCR) diagnostic tests have greatly improved, during last decades, our knowledge of the various viruses infecting major cucurbit crops worldwide (Lecoq, 2003). But for extensive surveys and to reduce their cost, there is the need for new simple and reliable mulitiplex techniques allowing detection of several viruses in a single operation in great numbers of samples (Boonham et al, 2014;Charlermroj et al, 2013;Lee et al, 2003;Wei, Pearson, Blohm, N€ olte, & Armstrong, 2009). …”

Section: Discussionmentioning

confidence: 99%

Control of Cucurbit Viruses

Lecoq¹,

Katis

2014

Advances in Virus Research

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“…The authors concluded that the sensitivity of detection is, among others, influenced by the proximity of the probe hybridization site to the unlabeled end of the targets. Wei et al (2009) developed a 25-mer oligonucleotide microarray targeting four distinct potyviruses that included 85 probes designed from conserved and variable sequence regions of the nuclear inclusion b (NIb) gene, RNA-dependent RNA polymerase (RdRp) gene, coat protein (CP) gene, and the 3′ untranslated region (UTR), specific to the four targeted potyviruses at both species and strain levels. Using “Combimatrix” platform 40-mer oligonucleotide probes, Tiberini et al (2010) designed a DNA microarray chip for screening 10 major economically important tomato viruses and later on this platform was optimized to include six pospiviroid species ( Tiberini and Barba, 2012 ).…”

Section: Molecular Hybridizationmentioning

confidence: 99%

Recent Advances on the Multiplex Molecular Detection of Plant Viruses and Viroids

2018

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Plant viruses are still one of the main contributors to economic losses in agriculture. It has been estimated that plant viruses can cause as much as 50 billion euros loss worldwide, per year. This situation may be worsened by recent climate change events and the associated changes in disease epidemiology. Reliable and early detection methods are still one of the main and most effective actions to develop control strategies for plant viral diseases. During the last years, considerable progress has been made to develop tools with high specificity and low detection limits for use in the detection of these plant pathogens. Time and cost reductions have been some of the main objectives pursued during the last few years as these increase their feasibility for routine use. Among other strategies, these objectives can be achieved by the simultaneous detection and (or) identification of several viruses in a single assay. Nucleic acid-based detection techniques are especially suitable for this purpose. Polyvalent detection has allowed the detection of multiple plant viruses at the genus level. Multiplexing RT polymerase chain reaction (PCR) has been optimized for the simultaneous detection of more than 10 plant viruses/viroids. In this short review, we provide an update on the progress made during the last decade on techniques such as multiplex PCR, polyvalent PCR, non-isotopic molecular hybridization techniques, real-time PCR, and array technologies to allow simultaneous detection of multiple plant viruses. Also, the potential and benefits of the powerful new technique of deep sequencing/next-generation sequencing are described.

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Development of a short oligonucleotide microarray for the detection and identification of multiple potyviruses

Cited by 23 publications

References 54 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

Control of Cucurbit Viruses

Recent Advances on the Multiplex Molecular Detection of Plant Viruses and Viroids

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