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

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.

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

“…Procedures to detect and identify various viruses or virus strains in a single assay simultaneously reduce time and cost of the analysis (see Pallás et al., 2018 for a comprehensive review), and are especially suitable for evaluating mixed infections in individual plants. The detection of individual viruses in a sample is mainly based on three approaches: i) spatial separation of detection sites (wells or spots); ii) separation of distinctly sized amplicons by electrophoresis; and iii) using a different label for each virus ( Dincer et al., 2017 ).…”

“…The last constriction can be avoided by using primers labeled with different color fluorescent dyes or coupling the PCR with hybridization with specific probes ( James et al., 2006 ). Multiplex PCR or RT-PCR have been used to identify: i) the main viruses infecting a particular crop, such as tomato, tobacco, legumes, potato, ornamentals, cucumber and olive ( Bariana et al., 1994 ; Bertolini et al., 2001 ; Dai et al., 2012 ; Panno et al., 2012 ; Ge et al., 2013 ; Ali et al., 2014 ; Pallás et al., 2018 ); ii) viruses from the same genus ( Uga and Tsuda, 2005 ; Hu et al., 2010 ; Panno et al., 2014 ); and iii) different strains of a viral species ( Hammond et al., 1999 ; Nie and Singh, 2003 ; Huang et al., 2004 ; Alfaro-Fernández et al., 2009 ; Bester et al., 2012 ). Multiplex real-time qPCR with Taqman probes labeled with different fluorescent dyes have been used to identify viruses from the same crop ( Abrahamian et al., 2013 ; López-Fabuel et al., 2013 ; Malandraki et al., 2017 ), and strains or isolates from the same viral species ( Varga and James, 2005 ; Debreczeni et al., 2011 ).…”

Field-Effect Sensors for Virus Detection: From Ebola to SARS-CoV-2 and Plant Viral Enhancers

“…Plant viruses are among the major contributors to economic losses in agriculture [more than 50 billion €/year worldwide (Pallás et al, 2018)]. Therefore, there is great interest in sensitive, rapid and easy-to-use portable devices for an early detection of viruses in infected plants by in-field or on-site application (Khater et al, 2017;Cassedy et al, 2020).…”

Molecular Detection of Potato Viruses in Bangladesh and Their Phylogenetic Analysis

“…As viruses are ubiquitous in nature, they are assumed as a major barrier for potato cultivation, particularly during mixed infection [ 4 , 5 , 6 ]. Worldwide, over 50 virus species have been recognized that affect potato production by reducing tuber yield of above 50% in the case of single infection, and which can reach beyond 80% during mixed infections, causing losses of over 50 billion euros annually [ 6 , 7 , 8 ]. In Bangladesh, a total of seven potato viruses, Potato leafroll virus (PLRV; family: Leutoviridae, genus: Polerovirus), Potato virus X (PVX; family: Alphaflexiviridae, genus: Potexvirus), Potato virus Y (PVY; family: Potyviridae, genus: Potyvirus), Potato virus S (PVS; family: Betaflexiviridae, genus: Carlavirus), Potato virus H (PVH; family: Betaflexiviridae, genus: Carlavirus), Potato virus M (PVM; family: Betaflexiviridae, genus: Carlavirus) and Potato virus A (PVA; family: Potyviridae, genus: Potyvirus) have been reported so far [ 9 , 10 , 11 , 12 ].…”

“…However, documentation of actual disease-causing agent is crucial for proper management program [ 18 ]. Detection of potato viruses at the initial stage is one of the best ways to control the disease development and virus free seed potato production [ 8 ]. The authentic detection of viruses in seed lot followed by destruction of infected tubers is an effective control strategy that inhibits virus infection in field [ 19 ].…”