Abstract
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.
Highlights
Plant viruses and viroids are still a major concern in modern agriculture
Polyvalent Detection of Viruses/Viroids of the challenges posed by the need for specific and sensitive detection of plant viruses and viroids (Lopez et al, 2009)
One of the most important challenges in plant virus/viroid diagnosis during the last decade has been the implementation of polyvalent and/or multiplex detection methods as these contribute to cost reductions, increased efficiency, and routine use (James et al, 2006)
Summary
Plant viruses and viroids are still a major concern in modern agriculture. They cause substantial economic losses in many important crops, especially those for which no virus-resistant varieties are available. Different approaches, based on different biochemical principles, can be used to detect simultaneously multiple plant viruses or viroids including the following: (i) multiplex or polyvalent polymerase chain reaction (PCR), (ii) molecular hybridization including array techniques, and (iii) next-generation sequencing (NGS) technologies The latter is revolutionizing the way plant virus diagnosticians are addressing the identification and characterization of new viruses and viroids and is having a profound impact on plant pathology in general (see Barba et al, 2014; Massart et al, 2014; Wu et al, 2015 for comprehensive reviews of NGS). PCR-based and molecular hybridization methods are still used frequently in most diagnostic laboratories due to years of validation, knowledge of their specificity and sensitivity, ease of implementation, and relatively low cost In this short review, we update the progress made during the last 12 years on the multiplex or broad-spectrum detection of plant viruses and viroids
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