Abstract
Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.
Highlights
Until recently, plant virus discovery appeared as a long and fastidious task, mainly driven by the need to identify the etiology of diseases of unknown origin
We aim to discuss the new challenges raised by next generation sequencing (NGS) as illustrated by case studies, and to suggest guidelines for researchers, policy makers, plant health authorities and plant inspection services by describing the necessary steps, the appropriate interactions and the inherent prioritization to be followed after discovering a new virus sequence [or a new isolate or variant, or (a) new host(s)]
NGS technologies pose new challenges to scientists and to plant health authorities when it comes to analyzing the risks associated with a new virus or pathogen, its potential to spread, or its economic impact and when trying to take a timely decision on whether to let go or destroy contaminated plant materials
Summary
Plant virus discovery appeared as a long and fastidious task, mainly driven by the need to identify the etiology of diseases of unknown origin. NGS technologies are progressively reaching the diagnostic field (Massart et al, 2014), impacting quarantine regulations (Martin et al, 2016) Their use allows the continuous discovery of new plant. Proposal: Framework for Characterisation of New Viruses viruses, the observation of an increasing diversity of variants for known viruses and the frequent existence of a complex of different viruses Downstream of these findings, the main challenge to be addressed is the biological significance (pathogenicity, hosts, transmission, epidemiology...) of the discovery of a novel virus species or strain in single plants, in asymptomatic plants and for viruses that are the founding members of new virus genera or families and share little or no sequence similarity with known viruses (Wu et al, 2015). The ability of NGS to detect cryptic (symptomless) viruses in cultivated and wild plants, and the reported mutualistic interactions challenging the traditional dogma that all viruses are pathogens (Roossinck, 2011), are adding new difficulties to the prediction of the impact of new viruses
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