1. A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologiesSébastien Massart, Thierry Candresse, José Gil, Christophe Lacomme, Lukas Predajna, Maja Ravnikar, Jean-Sébastien Reynard, Artemis Rumbou, Pasquale Saldarelli, Dijana Škorić, Eeva J. Vainio, Jari P. T. Valkonen, Hervé Vanderschuren, Christina Varveri, Thierry Wetzel, 2017, original scientific article 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.
Keywords: NGS, pest risk analysis, virus diseases, biological characterization, plant health, regulatory agencies
Published in DiRROS: 25.07.2024; Views: 93; Downloads: 54
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2. Increased diversity of citrus tristeza virus in EuropeJelena Zindović, Miroslav Čizmović, Ana Vučurović, Paolo Margaria, Dijana Škorić, 2023, original scientific article Abstract: This study investigated the genetic diversity of citrus tristeza virus (CTV) isolates from Montenegro and Croatia, European countries with the northernmost citrus growing regions situated on the Eastern Adriatic coast. Fifteen complete or nearly complete CTV genomes were reconstructed from high-throughput sequencing of samples collected in distinct municipalities in Montenegro and Opuzen municipality in Croatia. Phylogenetic analyses assigned some of the sequences to VT and T30 strains, previously recorded in Europe, while remarkably other isolates were placed in S1 and RB groups, which have not been reported in Europe so far. In addition, a new phylogenetic lineage including only isolates from Montenegro was delineated and tentatively proposed as the MNE cluster. Recombination analysis revealed evidence of 11 recombination events in the sequences obtained in this study, between isolates of related strains, within isolates of the same strain, and between distant strains. These findings show that CTV diversity in Europe is higher than reported before and calls for the re-evaluation of management strategies.
Keywords: complete genomes, genotyping, citrus tristeza virus, CTV, non-EU strain
Published in DiRROS: 29.03.2024; Views: 407; Downloads: 165
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