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.

Ensuring the reliability of diagnostic activities is an essential cornerstone of plant health strategies to reduce the risk of entry and spread of plant pests in a region and ultimately their impacts. Diagnostic tests should be validated to ensure that they are fit for purpose. Validation is usually done by diagnostic laboratories, although companies commercializing diagnostic kits also produce validation data for their products. Due to the high number of pest, matrix, and method combinations and given the significant resources required to validate tests, it is essential that validation data are shared with the entire diagnostic community and produced in a harmonized way to facilitate their use by different stakeholders. Indeed, the selection of tests to be used in specific contexts is not the sole responsibility of diagnostic laboratories but also involves national plant protection organizations. The VALITEST EU project (2018 to 2021) was established to tackle all these issues. New validation data for tests targeting important pests for the European and Mediterranean Plant Protection Organization region were produced. Guidelines to improve and harmonize the validation framework were developed. Sharing of validation data and experience was ensured through the development of new or existing databases, the organization of training courses, and the dissemination of the project outputs in scientific publications and standards. Finally, the involvement of researchers, diagnosticians, policy makers, inspectors, and industries and the establishment of the European Plant Diagnostic Industry Association were important actions to strengthen the interactions between plant health stakeholders. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Many scolytine beetle species have been expanding in new territories, travelling with wood and plants for planting, sometimes with a high impact on plant health. Here, we attempt to quantify the mobility of these species and to identify the biological drivers of mobility and impact. Mobility was estimated by counting the numbers of landmasses (contiguous pieces of land, surrounded by ocean or sea) colonised by each species. A series of potential drivers (taxonomic tribes; feeding regimes; polyphagy; reproductive strategy; host taxa; aggregation pheromones and long-range primary attractants), as well as impact on host health were recorded. A total of 163 species were identified, out of 5546 counted in the whole subfamily. The cosmopolitan taxa amongst the subfamily showed significant disharmony with regards to invasion frequency. Four tribes (Xyleborini; Ipini; Crypturgini; Hylastini) were significantly over-represented and two others (Corthylini; Hexacolini) were under-represented. Some 53% of the 163 species are inbreeding, a very significant excess as compared to the whole subfamily (29%). The inbreeders colonised more landmasses than the outbreeders. There is a significant relationship between the number of host families attacked by a species and the number of colonised landmasses. Most of the invasive species are recorded to respond to long-range host primary attractants, only one quarter respond to pheromones. All very mobile species respond to long-range primary attractants and none is known to respond to pheromones. Very mobile species are all associated with a substantial or moderate impact. The most mobile species belong to a limited number of subtribes. They are often inbreeding, polyphagous and respond to long-range primary attractants, but do not produce pheromones. However, there are many counter-examples. The outbreeding Scolytus multistriatus attacks only three host families, producing aggregation pheromones and has established in thirteen landmasses, with a high impact. Due to these many exceptions, species-based risk prediction relying on the few traits routinely analysed in literature suffers from important uncertainties.

Plant pests are a threat to biodiversity, food security, and the economy. The challenges posed by the introduction of plant pests have triggered the establishment of cooperative mechanisms such as the International Plant Protection Convention (IPPC), an international treaty to protect plant health, but also of Regional Plant Protection Organizations (RPPOs), such as the European and Mediterranean plant Protection Organizations (EPPO). RPPOs participate in activities in their regions to promote and achieve the objectives of the IPPC. Because accurate and reliable detection and identification of pests are essential in order to be able to take appropriate measures against a pest and thus avoid or reduce the economic, social, and environmental costs that it can cause, the IPPC and EPPO have established a specific program on diagnostics. The main aim of this article is to present the diagnostic activities conducted by the European and Mediterranean Plant Protection Organization and Euphresco. Some information is also presented on other initiatives in diagnostics.

High-throughput sequencing (HTS) technologies have the potential to become one of the most significant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests has been growing steadily for more than a decade and they are now envisioned as a routine diagnostic test to be deployed by plant pest diagnostics laboratories. Nevertheless, HTS technologies and downstream bioinformatics analysis of the generated datasets represent a complex process including many steps whose reliability must be ensured. The aim of the present guidelines is to provide recommendations for researchers and diagnosticians aiming to reliably use HTS technologies to detect plant pathogens and pests. These guidelines are generic and do not depend on the sequencing technology or platform. They cover all the adoption processes of HTS technologies from test selection to test validation as well as their routine implementation. A special emphasis is given to key elements to be considered: undertaking a risk analysis, designing sample panels for validation, using proper controls, evaluating performance criteria, confirming and interpreting results. These guidelines cover any HTS test used for the detection and identification of any plant pest (viroid, virus, bacteria, phytoplasma, fungi and fungus-like protists, nematodes, arthropods, plants) from any type of matrix. Overall, their adoption by diagnosticians and researchers should greatly improve the reliability of pathogens and pest diagnostics and foster the use of HTS technologies in plant health.

High-throughput sequencing (HTS) is a powerful tool that enables the simultaneous detection and potential identification of any organisms present in a sample. The growing interest in the application of HTS technologies for routine diagnostics in plant health laboratories is triggering the development of guidelines on how to prepare laboratories for performing HTS testing. This paper describes general and technical recommendations to guide laboratories through the complex process of preparing a laboratory for HTS tests within existing quality assurance systems. From nucleic acid extractions to data analysis and interpretation, all of the steps are covered to ensure reliable and reproducible results. These guidelines are relevant for the detection and identification of any plant pest (e.g. arthropods, bacteria, fungi, nematodes, invasive plants or weeds, protozoa, viroids, viruses), and from any type of matrix (e.g. pure microbial culture, plant tissue, soil, water), regardless of the HTS technology (e.g. amplicon sequencing, shotgun sequencing) and of the application (e.g. surveillance programme, phytosanitary certification, quarantine, import control). These guidelines are written in general terms to facilitate the adoption of HTS technologies in plant pest routine diagnostics and enable broader application in all plant health fields, including research. A glossary of relevant terms is provided among the Supplementary Material.

Appropriate statistical analysis of the validation data for diagnostic tests facilitates the evaluation of the performance criteria and increases the confidence in the conclusions drawn from these data. A comprehensive approach to analysing and reporting data from validation studies and inter-laboratory comparisons such as test performance studies is described. The proposed methods, including statistical analyses, presentation and interpretation of the data, are illustrated using a real dataset generated during a test performance study conducted in the framework of the European project, VALITEST. This analytical approach uses, wherever possible and whenever applicable, statistical analyses recommended by international standards illustrating their application to plant health diagnostic tests. The present work is addressed to plant health diagnosticians and researchers interested and/or involved in the validation of plant diagnostic tests, and also aims to convey the necessary information to those without a statistical background. Detailed statistical explanations are provided in the Appendices.

AbstractThe organisation of a test performance study (TPS) involves different steps that are mostly sequential, but some may be conducted simultaneously. This chapter details the following: the steps regarding the selection of the tests to be validated; the selection of the laboratories to participate in the TPS; the preparation of the materials and the dispatch of the samples; and the completion of the TPS (including the collection and analysis of the TPS results). The reader will be able to get the detailed information on how to define and plan timeline of the TPS, the appropriate number of samples (including replicates) and of laboratories that should be included in the TPS to ensure an appropriate statistical analysis, and how to perform basic analyses of the obtained data. In addition, this chapter covers the most important critical points which can endanger successful TPS organization providing the future TPS organisers in the field of plant health (but also in other similar fields) with the possibility to identify them in advance and carry-out successful TPS.

AbstractThe recent COVID-19 pandemic highlighted the importance of rapid and reliable pathogen detection. In the field of plant health accurate and timely detection is a corner stone for successful pest control. Plant pests can be diagnosed with a variety of tests, which may be developed by commercial companies or research institutions. The reliability of diagnostic tests depends on the intended use of the tests, their performance characteristics and associated uncertainty obtained from validation studies and the experience of the laboratories. The performance characteristics of tests are obtained during a process called validation. Performance characteristics that are frequently used to characterise tests include: analytical sensitivity, analytical specificity (inclusivity and exclusivity), selectivity, repeatability and reproducibility. The validation process requires significant investment in terms of human and financial resources and can be conducted by a single diagnostic laboratory or through interlaboratory comparisons. The purpose of this book is to provide practical and technical guidance for the organisation of test performance studies (TPS), which are one type of interlaboratory comparison where the performance of (a) test(s) (is)are assessed by two or more laboratories. The major steps and challenges faced during the preparation, organisation and reporting of TPS are identified and can be used by organisers of future TPS not only in the field of plant pest detection, but also in other areas.

AbstractThere are two types of interlaboratory comparison studies: proficiency tests, which aim at monitoring the proficiency of laboratories, and test performance studies (TPS), which aim at evaluating the performance of (a) specific test(s) and whether it (they) is (are) fit for purpose. This booklet covers only TPS organisation. A TPS is usually organised to monitor the performance of a newly developed test to detect and/or identify pests or to compare the performance of different tests. The results of TPS also provide information on how (a) test(s) perform(s) in different laboratories. This allows a better estimation of the accuracy and reproducibility of tests. Organising a TPS is a complex process that requires considerable effort from the organisers in terms of time, expertise, and finances. Therefore, the selection of e.g. pests and of participants are important steps which are described in this chapter It also discusses the minimum criteria that the TPS organiser should meet.

VALITEST is an EU‐funded project built to improve the reliability of diagnostic tests performed in plant health laboratories across the European and Mediterranean region. The project is undertaken by a consortium of 16 partners composed of research institutions, private companies (such as diagnostic kit providers), national plant protection organizations and one intergovernmental organization (EPPO). Current harmonized procedures for the validation and organization of test performance studies will be improved based on the experience gained from the project and by including appropriate statistical approaches, by adapting the process for new promising technologies (e.g. high‐throughput sequencing) and by providing new guidelines for the production of reference materials for validation studies. The project will provide a more complete and precise description of the performance of 82 diagnostic tests targeting 11 pests of interest for stakeholders of the region. It will also tackle the need for proficient users by developing a horizontal approach for the evaluation of laboratories’ proficiency and by organizing training activities on the concept of validation. The outcomes of the project will stimulate, optimize and strengthen the interactions between stakeholders in plant health for better diagnostics and lay the foundations for structuring the quality and the commercial offers for plant health diagnostics tools thanks to the creation of a dedicated association and a quality charter.

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.

One of the main aims of EPPO is to help its member countries to prevent entry or spread of dangerous pests (plant quarantine). The Organization has therefore been given the task of identifying pests which may present a risk (early warning/horizon scanning), evaluating their risk for the region and making proposals on the phytosanitary measures which can be taken against them (Pest Risk Analysis). Standards are also developed, including standards on how to eradicate and control pests. In addition to the development of Standards, activities on communication and citizen science (development of guidelines on raising public awareness and the production of toolkits to use in raising awareness campaigns) have also recently been started. The EPPO Secretariat was alerted by the National Plant Protection Organization (NPPO) of Sweden in 2003, and Norway in 2010, to two potential new pests, Emerald ash borer (EAB), Agrilus planipennis (Fairmaire) and Bronze birch borer, Agrilus anxius (Gory) respectively. Because of the importance of these two pests for forest species in the EPPO region, member countries agreed that EPPO recommendations should be prepared. The different EPPO activities relevant to A. planipennis and A. anxius are presented, highlighting the challenges they currently pose to the region.

Many bark and ambrosia beetle species (Coleoptera: Scolytinae and Platypodinae) are known to have spread worldwide in relation to international trade. Concerns have been expressed within the European and Mediterranean Plant Protection Organization (EPPO) about recent introductions of non-indigenous species of these groups. Regulation of the non-coniferous wood trade into many EPPO member countries is currently not sufficient to cover such risks. In 2018–2019, an EPPO study on the risk of bark and ambrosia beetles associated with imported non-coniferous wood was carried out, and the key characteristics contributing to the pest risk from introduced species were determined using expert consensus. This paper summarizes the key findings of the study, which are available in full detail on the EPPO website. The study identified biological and other risk factors and illustrated them with examples from 26 beetle species or groups of species known to be invasive or posing a threat to plant health. These representative species were classified into three categories based on known damage and level of uncertainty. In the present article, factorial discriminant analyses were used to identify features of bark and ambrosia beetle biology associated with damage caused and invasiveness. Based on the information assembled and consideration of the risk factors, it was recommended that in order to prevent the introduction of new bark and ambrosia beetles via non-coniferous wood commodities, horizontal phytosanitary measures should be adopted, irrespective of the host plant species and the origin (i.e., for all genera of non-coniferous woody plants and from all origins). Phytosanitary measures are presented here for various wood commodities.

Reliable and rapid diagnostic methods are essential to support inspection activities conducted by National Plant Protection Organizations (NPPOs) in the framework of their official mandate, and to evaluate the efficacy of control measures taken. Since 1998 the European and Mediterranean Plant Protection Organization (EPPO) has been supporting the harmonization of diagnostic methods for regulated pests in the EPPO region through the development of technical standards. In order to increase active collaboration among the organizations involved in plant health research activities at the national and regional levels, Euphresco (European Phytosanitary Research Coordination) was established in 2006 and funded by the EU as an ERA-NET project. Euphresco has subsequently evolved into a self-sustaining international network hosted by EPPO. This paper describes the EPPO diagnostic programme. It will also provide some examples of research projects funded through Euphresco that have provided valuable support for the development of pest-specific diagnostic protocols and will show how NPPOs can shape the research agenda of research funders and help to identify gaps to be addressed through transnational collaboration.

Reliable and rapid diagnostic methods are essential to support inspection activities conducted by National Plant Protection Organizations (NPPOs) in the framework of their official mandate, and to evaluate the efficacy of control measures taken. Since 1998 the European and Mediterranean Plant Protection Organization (EPPO) has been supporting the harmonization of diagnostic methods for regulated pests in the EPPO region through the development of technical standards. In order to increase active collaboration among the organizations involved in plant health research activities at the national and regional levels, Euphresco (European Phytosanitary Research Coordination) was established in 2006 and funded by the EU as an ERA-NET project. Euphresco has subsequently evolved into a self-sustaining international network hosted by EPPO. This paper describes the EPPO diagnostic programme. It will also provide some examples of research projects funded through Euphresco that have provided valuable support for the development of pest-specific diagnostic protocols and will show how NPPOs can shape the research agenda of research funders and help to identify gaps to be addressed through transnational collaboration.