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

Luis Rubio,Luis Galipienso,Inmaculada Ferriol

doi:10.3389/fpls.2020.01092

Abstract

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.

Highlights

Viral diseases are a major threat to sustainable and productive agriculture worldwide, resulting in losses of several billion dollars every year (Mumford et al, 2016)
The current state and progress of procedures used for virus detection are reviewed, discussing important features such as their sensitivity, specificity, versatility, portability, capacity for multiplexing, and virus quantification and designability
Damages caused by pests and diseases have a considerable negative economic impact in agriculture, being emergent viral diseases important (Anderson et al, 2004; Mumford et al, 2016)

Summary

Introduction

Viral diseases are a major threat to sustainable and productive agriculture worldwide, resulting in losses of several billion dollars every year (Mumford et al, 2016). The main factors driving virus emergence are: i) the agricultural systems based on monocrops with low genetic diversity and high plant density, which are more vulnerable to pathogens and pests; ii) world trade of plant material (germplasm and live plants) that moves viruses, hosts, and vectors to new regions and environments; iii) the climate change affecting the distribution area of hosts and vectors; and iv) the ability of viruses for rapid evolution and adaptation (Anderson et al, 2004; Jones, 2009; Elena et al, 2014). This review includes basic concepts of genetic diversity and evolution of plant viruses and how they must be considered to improve detection. This review follows a pragmatic approach aimed to guide plant pathologists to design and apply more accurate detection procedures for a more efficient management of viral diseases

Methods

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Conclusion