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Classification and characterization of plant viruses identified by metagenomics approaches

Judith Brown: School of Plant Sciences, University of Arizona

<div>The application of genomic pathology tools for the ‘discovery’ of new and emerging plant viruses is expected to have far-reaching effects in the field of plant virology. Advancements in metagenomics have created unprecedented potential for discovering previously unknown or unrecognizable viruses infecting plants on land and in the seas. However, is not clear how annotation of coding regions or the assignment of gene function for the anticipated plethora of genomic variants will be accomplished, in part, because most will not be established in culture, cloned, or archived as in the past. For pathogenic viruses, this could delay proof of causality and timely fundamental studies. Also, the sheer number of viral genome sequences destined for public databases is expected to grow exponentially, requiring additional storage, and increased capacity in taxonomic frameworks for already-recognized and entirely new taxa. Further, the pace at which the criteria guiding taxonomic classification and rules of nomenclature will substantially accelerate. At the same time, metagenomics technologies offer enormous potential for uncovering the dynamics of entire viral populations, in near, real-time. Such information, shared through global networks, could reduce viral spread or prevent outbreaks altogether. Use of extensive sequence databases will accelerate the association of new viruses with outbreaks and of arthropod or other vectors with transmission, leading to expedited disease management with increased precision. The rapid expansion in ‘viral genome real estate’ is creating exciting, new possibilities for mining uncharted territories to expand fundamental knowledge in plant virology, and facilitate timely discovery, tracking, and management of viral diseases.</div>