The game-changing impact of NGS in Plant Virology
Thierry Candresse: INRA Bordeaux, UMR 1332 BFP
<div>In the past few years, the rapid development of high-throughput sequencing (HTS) technologies has impacted many research areas. In virology and, in particular, in plant virology, HTS coupled with bioinformatics have dramatically changed the way virus discovery, etiology efforts or viral population analyses are performed. Among the advantages of such approaches is that they offer for the first time the ability to perform the complete viral indexing of a plant sample without the need for any prior knowledge. Protocols for the efficient analysis of a variety of templates including siRNAs, virion-associated nucleic acids (VANA), double-stranded RNAs (dsRNAs), mRNAs or total RNAs, with or without rRNA depletion, are now available, together with efficient pipelines for the bioinformatics analysis of the huge volumes of sequence data involved. As a consequence, a wide range of novel plant viruses have been described, a first glimpse at phytoviromes has been achieved and some viral populations have been described with unprecedented precision and depth. These technologies have a huge potential in certification and for the improvement of the safety of the conservation and movement of plant materials. Still, HTS-based viral indexing has yet to be applied on a large scale in routine diagnostic settings with the need to meet challenges such as validation, comparison of sensitivity with existing techniques or implementation of quality controls.</div>
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