1. Development of draft Standard Operating Procedures (SOPs) available for the production of the reference materials identified in task 3.1 : grant agreement N. 773139Anne-Marie Chappé, A Chabirand, P. Dahlin, C. de Krom, Tanja Dreo, Pascal Gentit, L Laurenson, F. Peter, D. Spadaro, A.D. van Diepeningen, René van der Vlugt, E. van Veen, Marcel Westenberg, 2019, treatise, preliminary study, study Abstract: A general standard operating procedure (SOP) for the production of reference material (RM) for use in plant health diagnostics was developed. The general SOP was designed based on (limited) information on existing SOPs and guidelines available with the consortium partners. The general SOP describes the different steps required in the production process, ranging from the different possible sources of the reference material, tests to confirm its identity, possibly required multiplication steps to the actual production process. For each step in the process, criteria and critical points are identified. The criteria that reference material has to meet, and their minimum required levels as identified and described in Deliverable 3.1 of WP3 form an import basis of the final production process.
Keywords: plant health diagnostics
Published in DiRROS: 03.09.2024; Views: 115; Downloads: 49
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2. 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: 217; Downloads: 112
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3. 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, original scientific article Abstract: 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.
Keywords: plant viruses and viroids, high throughput sequencing (HTS), biological characterization, plant health, regulatory agencies, Pest Risk Analysis (PRA), virus disease
Published in DiRROS: 12.07.2024; Views: 219; Downloads: 107
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4. Challenges and solutions in early detection, rapid response and communication about potential invasive alien species in forestsMaarten De Groot, Richard O'Hanlon, Erin Bullas-Appleton, György Csóka, Ágnes Csíszár, Massimo Faccoli, Eugenio Gervasini, Natalia Kirichenko, Márton Korda, Aleksander Marinšek, Nikki Robinson, Craig Shuttleworth, Jon Sweeney, Elena Tricarico, Laura Verbrugge, David Williams, Simon Zidar, Jana Kus Veenvliet, 2020, review article Abstract: Invasive alien species (IAS) are an important threat to forests. One of the best ways to manage potential IAS is through early detection and rapid response (EDRR) strategies. However, when dealing with IAS in forests, EU regulations are divided between phytosanitary regulations and IAS regulations. A version of EDRR for the former has been in place in the EU for more than 15 years while the latter is still in the process of being implemented. During 2019, a workshop was held to gather international experts on different plant health pests and IAS. The purpose of this workshop was to identify the opportunities and difficulties in applying the EDRR system in the EU phytosanitary and IAS legislation to four species for providing suggestions to improve the EDRR system. The model species are well known and come from different trophic levels. These species were the American pokeweed (Phytolacca americana), the grey squirrel (Sciurus carolinensis); and the plant health pests Geosmithia morbida and Emerald ash borer (Agrilus planipennis). We identified the similarities in the challenges of early detection, rapid response and communication of these species. For all species, difficulties in species identification, knowledge gaps on the pathways of spread, a lack of resources and uncertainty over which national government service was the competent authority were identified as the main challenges. Other challenges like public perception for the grey squirrel or methodological problems were species-specific. Regarding the rapid response: public perception, determination of the eradication area, sufficient scientific capacity and the lack of resources were common challenges for all species. Therefore, collaboration between institutes dealing with plant health pests and IAS can lead to better control of both groups of unwanted %organisms in forests.
Keywords: early warning system, plant health legislation, EU IAS legislation, alien species, Geosmithia morbida, Emerald ash borer, American pokeweed, Grey squirrel, rapid response system
Published in DiRROS: 11.12.2020; Views: 1879; Downloads: 754
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5. Using citizen science to monitor the spread of tree pests and diseases : outcomes of two projects in Slovenia and the UKPeter Crow, Ana Pérez-Sierra, Andreja Kavčič, Kate Lewthwaite, Marija Kolšek, Nikica Ogris, Barbara Piškur, Jana Kus Veenvliet, Simon Zidar, Suzanne Sancisi-Frey, Maarten De Groot, 2020, original scientific article Abstract: The trees and forests of Europe are increasingly under threat from new pests and diseases that have originated in other parts of the world. Early detection of alien species when they first appear in European countries allows rapid response and offers the best chance to mitigate against their establishment and spread. Citizen science initiatives such as LIFE ARTEMIS in Slovenia, and Observatree in the UK, provide members of the public with the necessary training and educational resource to identify these tree pests and diseases and report them to the appropriate authorities, thereby increasing the level of surveillance and the capacity of the early warning system. This paper summarises some of the outcomes of these two projects and how they have both become integral parts of the official forest and tree health monitoring systems within their respective countries of Slovenia and the United Kingdom.
Keywords: invasive alien species, plant health, tree health, forest health, early warning, rapid response
Published in DiRROS: 16.11.2020; Views: 1986; Downloads: 1017
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6. Towards a better early detection and rapid response system against invasive alien species in forestsMaarten De Groot, Jana Kus Veenvliet, Nikica Ogris, Aleksander Marinšek, Lado Kutnar, 2020, preface, editorial, afterword Keywords: invasive alien species, plant health, tree health, forest health, early warning, rapid response
Published in DiRROS: 16.11.2020; Views: 1665; Downloads: 874
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