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.

PCR has been the major a breakthrough leading successful detection RNA/DNA viruses. The development of qPCR assays helped to avoid the risk of post-PCR contamination and has benefits of high reproducibility and accuracy. The nonthermal methods, like HDA, RPA, NASBA, etc., have proved suitable for poorly resourced laboratories and on-site testing. NGS technology involving massive parallel sequencing approach followed by bioinformatics analysis has revolutionized discovery of novel viruses. With the increasing competition for machinery and analytical reagents among companies, high-throughput multiplexing and virus detection techniques are becoming cheaper. However, the challenge remains in their use at the site ensuring to maintain highest crop health standards at affordable price.

Journal of Antivirals & Antiretrovirals is using Editorial Manager System for quality in review process. Editorial Manager is an online manuscript submission, review and tracking systems used by most of the best open access journals. Review processing is performed by the editorial board members of journal or outside experts; at least two independent reviewers approval followed by editor's approval is required for acceptance of any citable manuscript.

Send your manuscript at www.longdom.org/submissions/antivirals-antiretrovirals.html or as an e-mail attachment to our Editorial Office at manuscripts@longdom.org