A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

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.

[1]  R. Roberto,et al.  A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris. , 2012, Virus research.

[2]  Eugene V Koonin,et al.  New dimensions of the virus world discovered through metagenomics. , 2010, Trends in microbiology.

[3]  M. Fuchs,et al.  Control of viruses infecting grapevine. , 2015, Advances in virus research.

[4]  Virus infection decreases the attractiveness of white clover plants for a non-vectoring herbivore , 2012, Oecologia.

[5]  S. Ghabrial,et al.  Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes , 2010, Journal of Virology.

[6]  Yongjiang Zhang,et al.  Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. , 2015, Annual review of phytopathology.

[7]  L. Sumner,et al.  Virus infection improves drought tolerance. , 2008, The New phytologist.

[8]  S. Massart,et al.  Current impact and future directions of high throughput sequencing in plant virus diagnostics. , 2014, Virus research.

[9]  I. Tzanetakis,et al.  Quarantine Regulations and the Impact of Modern Detection Methods. , 2016, Annual review of phytopathology.

[10]  M. Roossinck.  The good viruses: viral mutualistic symbioses , 2011, Nature Reviews Microbiology.

[11]  Akhtar Ali,et al.  A simple technique for separation of Cowpea chlorotic mottle virus from Cucumber mosaic virus in natural mixed infections. , 2008, Journal of virological methods.

[12]  S. Bargen,et al.  Cherry leaf roll virus abundant on Betula pubescens in Finland , 2007 .

[13]  J. R. Úrbez-Torres,et al.  Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses , 2010, Archives of Virology.

[14]  A. Katzourakis,et al.  Endogenous viruses: Connecting recent and ancient viral evolution. , 2015, Virology.

[15]  J. Syller,et al.  Antagonistic within-host interactions between plant viruses: molecular basis and impact on viral and host fitness. , 2016, Molecular plant pathology.

[16]  S. Satar,et al.  Identification and characterization of citrus yellow vein clearing virus, a putative new member of the genus Mandarivirus. , 2012, Phytopathology.

[17]  J. Burger,et al.  Identification and distribution of multiple virus infections in Grapevine leafroll diseased vineyards , 2015, European Journal of Plant Pathology.

[18]  M. Fuchs,et al.  Grapevine red blotch-associated virus Is Widespread in the United States. , 2014, Phytopathology.

[19]  M. Mohiuddin,et al.  Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis , 2015, Front. Microbiol..

[20]  M. Sudarshana,et al.  Detection of a New Luteovirus in Imported Nectarine Trees: A Case Study to Propose Adoption of Metagenomics in Post-Entry Quarantine. , 2015, Phytopathology.

[21]  S. Elena,et al.  Application of game theory to the interaction between plant viruses during mixed infections. , 2009, The Journal of general virology.

[22]  I. Adams,et al.  Carrot yellow leaf virus Is Associated with Carrot Internal Necrosis , 2014, PloS one.

[23]  Neil Boonham,et al.  Methods in virus diagnostics: from ELISA to next generation sequencing. , 2014, Virus research.

[24]  L. Domier,et al.  Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes. , 2016, Virus research.

[25]  Z. Šubr,et al.  Infectious full-length clones of plant viruses and their use for construction of viral vectors. , 2007, Acta virologica.

[26]  Rana Demiral,et al.  High genetic diversity at the inter-/intra-host level of Cherry leaf roll virus population associated with the birch leaf-roll disease in Fennoscandia , 2016 .

[27]  T. Candresse,et al.  New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing , 2016, PloS one.

[28]  T. Mekuria,et al.  High-Throughput Sequencing Identifies Novel Viruses in Nectarine: Insights to the Etiology of Stem-Pitting Disease. , 2016, Phytopathology.

[29]  I. Gutiérrez-Aguirre,et al.  A new application of monolithic supports: the separation of viruses from one another. , 2015, Journal of chromatography. A.

[30]  Varvara I. Maliogka,et al.  TAXONOMIC REVISION OF THE FAMILY CLOSTEROVIRIDAE WITH SPECIAL REFERENCE TO THE GRAPEVINE LEAFROLL-ASSOCIATED MEMBERS OF THE GENUS AMPELOVIRUS AND THE PUTATIVE SPECIES UNASSIGNED TO THE FAMILY , 2012 .

[31]  P. Bianchedi,et al.  Genetic Variability of Grapevine Pinot gris virus and Its Association with Grapevine Leaf Mottling and Deformation. , 2015, Phytopathology.