801. TESTING OF CHRYSANTHEMUM STEM NECROSIS VIRUS AND OTHER AMERICAN CLADE 1 TOSPOVIRUSES BY RT-PCR : validation reportNataša Mehle, Irena Bajde, Jakob Brodarič, Ana Vučurović, 2024, final research report Abstract: Detection of Chrysanthemum stem necrosis virus (CSNV) and other tospoviruses of American
clade 1.
Keywords: CSNV, orthotospovirses, diagnostics, method validation, EURL-Virology
Published in DiRROS: 02.09.2024; Views: 271; Downloads: 122
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802. Deliverables 4 & 6 : refinement of pesticide risk assessment of amphibians and reptiles based on ecology and biology of wild populationsMarta Biaggini, Miguel A. Carretero, Dan Cogalniceanu, Mathieu Denoël, Christoph Leeb, Valentin Mingo, Gianpaolo Montinaro, Anamarija Žagar, 2024, final research report Abstract: Amphibians and reptiles are among the most threatened vertebrate taxa worldwide. About 41% (34%- 51%) of amphibians and 21% (18%-33%) of reptiles are included in the IUCN categories of threatened species (Critically Endangered, Endangered or Vulnerable; IUCN, 2021; Cox et al., 2022). In Europe, nearly a quarter of amphibians and one fifth of reptiles are threatened and a further 17% of amphibians and 13% of reptiles are included among the Near Threatened species (IUCN, 2021). There are multiple reasons why amphibians and reptiles are declining, but habitat loss and degradation, followed by chemical pollution, both mainly attributable to the expansion of intensive agriculture, are commonly indicated among the major causes of herpetofauna decline worldwide as well as in the European region (Gibbons et al., 2000; Collins and Storfer, 2003; Ribeiro et al., 2009; Todd et al., 2010; Böhm et al., 2013, Arntzen et al., 2017).
Keywords: reptiles, amphibians, pesticides, risk assessment, environmental protection
Published in DiRROS: 02.09.2024; Views: 287; Downloads: 150
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805. Marine strategy framework directive : Descriptor 2, non - indigenous species delivering solid recommendations for setting threshold values for non-indigenous species pressure on European seasKonstantinos Tsiamis, Ivan Cvitković, Marija Despalatović, Branko Dragičević, Jakov Dulčić, Ana Fortič, Janja Francé, Lovrenc Lipej, Borut Mavrič, Patricija Mozetič, Živana Ninčević Gladan, Martina Orlando-Bonaca, Monika Peterlin, Valentina Pitacco, Domen Trkov, Olja Vidjak, Ante Žuljević, 2021, final research report Abstract: Marine Non-Indigenous Species (NIS) are animals and plants introduced accidently or deliberately into the European seas, originating from other seas of the globe. About 800 marine non-indigenous species (NIS) currently occur in the European Union national marine waters, several of which have negative impacts on marine ecosystem services and biodiversity. Under the Marine Strategy Framework Directive (MSFD) Descriptor 2 (D2), EU Member States (MSs) need to consider NIS in their marine management strategies. The Descriptor D2 includes one primary criterion (D2C1: new NIS introductions), and two secondary criteria (D2C2 and D2C3). The D2 implementation is characterized by a number of issues and uncertainties which can be applicable to the Descriptor level (e.g. geographical unit of assessment, assessment period, phytoplanktonic, parasitic, oligohaline NIS, etc.), to the primary criterion D2C1 level (e.g. threshold values, cryptogenic, questionable species, etc), and to the secondary criteria D2C2 and D2C3. The current report tackles these issues and provides practical recommendations aiming at a smoother and more efficient implementation of D2 and its criteria at EU level. They constitute a solid operational output which can result in more comparable D2 assessments among MSs and MSFD regions/subregions. When it comes to the policy-side, the current report calls for a number of different categories of NIS to be reported in D2 assessments, pointing the need for the species to be labelled/categorised appropriately in the MSFD reporting by the MSs. These suggestions are proposed to be communicated to the MSFD Working Group of Good Environmental Status (GES) and subsequently to the Marine Strategy Coordination Group (MSCG) of MSFD. Moreover, they can serve as an input for revising the Art. 8 Guidelines.
Published in DiRROS: 02.09.2024; Views: 263; Downloads: 208
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806. Guidance document on multiplex real-time PCR methods : European Network of GMO LaboratoriesLutz Grohmann, Alessandra Barbante, Ronnie Eriksson, Francesco Gatto, Tzveta Georgieva, Ingrid Huber, Julie Hulin, René Köppel, Ugo Marchesi, Lucas Marmin, Marco Mazzara, Frank Narendja, Heather Owen, Elena Perri, Ingrid Scholtens, Tereza Sovová, Slawomir Sowa, Dejan Štebih, Christopher Weidner, Kamila Zdeňková, 2021, final research report Abstract: This document provides guidance for the development of new qualitative and quantitative multiplex real-time methods (mpPCR) and their implementation in a routine testing laboratory for food, feed and seeds. When implementing a mpPCR method, the laboratory should perform either an (in-house) validation or a verification of the method before its use.
The various method performance parameters of the specific requirements for mpPCR are described and examples are given. Several different aspects have been considered, including the selection of the fluorophores, the master mix and the real-time PCR instrument used. The technical aspects are examined and recommendations are made on the choice of the detection and quantification strategy. Finally, a separate chapter is dedicated to troubleshooting (e.g. underperforming method, no or poor signal strength, cross-talk).
In addition, a collection of existing mpPCR methods with emphasis on GMO detection is presented.
Published in DiRROS: 02.09.2024; Views: 327; Downloads: 1243
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807. Establishing thresholds : workshop on the MSFD Newly Introduced NIS (D2C1)Chiara Magliozzi, C. Bartilotti, A. Botelho, M. Bugeja, João Canning-Clode, Ana Fortič, Martina Orlando-Bonaca, 2023, final research report Abstract: The Workshop on ‘Establishing thresholds: workshop on the Marine Strategy Framework Directive (MSFD) Newly Introduced Non-Indigenous Species (NIS) (D2C1)’ took place online on the 24th November 2022, aiming at discussing and making progress towards establishing threshold values for the criterion D2C1. The workshop was organised by the Joint Research Centre (JRC), in collaboration with representatives of the Regional Sea Conventions (RSCs), under the MSFD Descriptor 2 Core Group, in the context of the MSFD Common Implementation Strategy Good Environmental Status Working Group. The participants to the workshop included academic and public authorities’ experts on MSFD NIS, RSCs representatives, the European Environment Agency (EEA), and Commission services. The workshop enabled sharing information on the state-of-the-art approaches on monitoring and assessment of D2C1 within Regional Seas and on the application of the time series analysis as a follow-up to Tsiamis et al. (2021) recommendations for setting threshold values. The discussion focused on ensuring comparability of approaches, how to account for uncertainties, and on areas for improvement. It was acknowledged that activities of RSCs are instrumental in coordinating the science and management of marine NIS. The various levels of monitoring across the North-East Atlantic Ocean, the Mediterranean Sea, the Baltic Sea and the EU Countries explain different methodological approaches for setting thresholds, while the limited monitoring restrict the application of these methodologies in the Black Sea. The workshop identified four main areas for improvements: i) establishment of acknowledged baselines for NIS introductions, ii) make further progress in monitoring and analysis methods, iii) agree on thresholds for new NIS introductions and, iv) ensure coherence and consistency between national and regional reports. The JRC will seek for opportunities to discuss and advance on identified areas for improvement with the MSFD national appointed NIS experts The MSFD Descriptor 2 (D2) Core Group will contribute to the discussions.
Keywords: Marine Strategy Framework Directive, MSFD, non-indigenous species, NIS, descriptor 2, marine biology, European Commission
Published in DiRROS: 02.09.2024; Views: 296; Downloads: 167
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809. Detection of food and feed plant products obtained by targeted mutagenesis and cisgenesisSlawomir Sowa, Alessandra Barbante, Wim Broothaerts, Malcolm Burns, Frédéric Debode, Marzia De Giacomo, Marc De Loose, Tina Demšar, Kolja Eckermann, Marie Alice Fraiture, 2023, final research report Abstract: The current EU legislation on GMOs and GM food and feed requires analytical testing to support traceability of these products on the market. The European Network of GMO Laboratories has reviewed the implications of the analytical requirements when they are applied to plant products developed with the use of new genomic techniques, i.e. targeted mutagenesis and cisgenesis. This review concluded that analytical testing to support traceability is not considered feasible for all products obtained by targeted mutagenesis and cisgenesis, both due to technical restrictions and because of implementation issues.
Keywords: new genomic techniques, detection in food and feed, targeted mutagenesis, cisgenesis
Published in DiRROS: 02.09.2024; Views: 272; Downloads: 504
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810. The International cookbook for wastewater practitioners : testing wastewater for public health, SARS-CoV-2Bernd Manfred Gawlik, Sara Comero, Daniel A. Deere, Gertjan Medema, Ismahane Remonnay, Jean-François Loret, Ana Maria de Roda Husman, Stephanie Rinck-Pfeiffer, Shelesh Agrawal, Ion Gutiérrez-Aguirre, 2024, final research report Abstract: During the 2020-2023 COVID-19 Global Public Health Emergency of International Concern, rapid progress was made with the application of Wastewater-Based Surveillance (WBS) (also known as Wastewater-Based Epidemiology (WBE)) to provide population-scale evidence of SARS-CoV-2 shedding into wastewater. The information gained was used to help monitor, communicate, and manage the COVID-19 pandemic.
Rapid and significant innovations in the field of WBS were realised in parallel in multiple jurisdictions globally. Global collaboration resulted in step-change improvements in multiple aspects of WBS simultaneously, including: health sector leadership; integration with public health surveillance; social and ethical guidance; high-level tactical wastewater catchment sampling strategies; wastewater sampling techniques; transport and storage of samples; laboratory analysis; normalisation and standardisation; data analysis and interpretation; and communication of results.
Innovations in WBS relating to COVID-19 continue to take place, and the benefits of those improvements are now being applied to other targets, such as other pathogens and genes. There are many journal articles and other publications describing these innovations. However, valuable lessons from the COVID-19 pandemic for WBS have not been systematically documented into a practical and readily digestible format.
The purpose of this ‘Cookbook’ is to provide practical and proven ‘recipes’ for WBS for SARS-CoV-2 for two reasons: firstly to help those considering new or extended WBS programmes targeting SARS-CoV-2; and secondly to provide a valuable record of what has been learned from the 2020- 2023 period to help inform WBS programmes to respond to future pandemics and for surveillance of other targets.
The Cookbook is structured into eight parts: 1. Introduction; 2. High-level Overview; 3. Health Sector Perspectives; 4. Methods and Methodologies - From data to action; 5. Methods and Methodologies - Measurement and testing; 6. Methods and Methodologies - Sampling; 6. Methods and Methodologies - Transportation protocols; 8. Conclusions. Multiple authors have contributed to each part, primarily from the European Union, as well as others from the global community of practice.
The Cookbook has been drafted by a global team of authors, with one or more lead authors identified for each chapter and working with their co-authors. The chapters were then subjected to extensive peer review from the external review group. These authors and reviewers are acknowledged in the Cookbook.
Keywords: coronavirus disease, disease surveillance, innovation, public health, report, sampling, standardisation, testing, wastewater
Published in DiRROS: 02.09.2024; Views: 298; Downloads: 212
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