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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: NGS, pest risk analysis, virus diseases, biological characterization, plant health, regulatory agencies
Objavljeno v DiRROS: 25.07.2024; Ogledov: 216; Prenosov: 112
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2. Managing the deluge of newly discovered plant viruses and viroids : an optimized scientific and regulatory framework for their characterization and risk analysisNuria Fontdevila Pareta, Maryam Khalili, Ayoub Maachi, Mark Paul Selda Rivarez, Johan Rollin, Ferran Salavert Pamblanco, Coline Temple, Miguel A. Aranda, Denis Kutnjak, Maja Ravnikar, 2023, izvirni znanstveni članek Povzetek: The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
Ključne besede: plant viruses and viroids, high throughput sequencing (HTS), biological characterization, plant health, regulatory agencies, Pest Risk Analysis (PRA), virus disease
Objavljeno v DiRROS: 12.07.2024; Ogledov: 213; Prenosov: 104
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3. Forewarned is forearmed : harmonized approaches for early detection of potentially invasive pests and pathogens in sentinel plantingsCarmen Morales-Rodríguez, Sten Anslan, Marie-Anne Auger-Rozenberg, Sylvie Augustin, Yuri Baranchikov, Amani Bellahirech, Daiva Burokiene, Dovile Čepukoit, Ejup Çota, Kateryna Davydenko, Maarten De Groot, 2019, izvirni znanstveni članek Povzetek: The number of invasive alien pest and pathogen species affecting ecosystem functioning, human health and economies has increased dramatically over the last decades. Discoveries of invasive pests and pathogens previously unknown to science or with unknown host associations yet damaging on novel hosts highlights the necessity of developing novel tools to predict their appearance in hitherto naïve environments. The use of sentinel plant systems is a promising tool to improve the detection of pests and pathogens before introduction and to provide valuable information for the development of preventative measures to minimize economic or environmental impacts. Though sentinel plantings have been established and studied during the last decade, there still remains a great need for guidance on which tools and protocols to put into practice in order to make assessments accurate and reliable. The sampling and diagnostic protocols chosen should enable as much information as possible about potential damaging agents and species identification. Consistency and comparison of results are based on the adoption of common procedures for sampling design and sample processing. In this paper, we suggest harmonized procedures that should be used in sentinel planting surveys for effective sampling and identification of potential pests and pathogens. We also review the benefits and limitations of various diagnostic methods for early detection in sentinel systems, and the feasibility of the results obtained supporting National Plant Protection Organizations in pest and commodity risk analysis.
Ključne besede: alien invasive pests, alien invasive pathogens, commodity risk analysis, early warning, sampling techniques, sentinel plants, pest risk analysis, prediction
Objavljeno v DiRROS: 01.07.2019; Ogledov: 2589; Prenosov: 1545
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