Viral diseases can cause severe losses to vegetable crop production which has an estimated annual value of 34,5 billion EUR in Europe. Therefore several billions are lost every year due to the prominence of viral diseases and the emergence of new viruses in European fields and greenhouses. Importantly viral diseases also lead to the extensive use of pesticides, thereby exposing European growers and consumers to pesticide residues. In relation to the work programme, the project aims at developing rapid and lasting solutions to emerging viral diseases caused by begomoviruses (whitefly-transmitted) and tobamoviruses (mechanically transmitted) on cucurbits and tomato in Northern Europe and the Mediterranean Basin as well as at increasing knowledge to better control and manage the viral diseases. The project is structured in 6 objectives : 1. Knowledge sharing and engagement of stakeholders in research activities (Short term impact) 2. Develop robust diagnostic tests, quarantine measures and identify ecological factors driving disease outbreaks (Short term impact) 3. Understand plant-virus(es)-vector interactions (Medium term impact) 4. Develop IPM solutions (Medium term impact) 5. Pyramidize natural resistance (Long term impact) 6. Train the value chain (Medium term impact) The objectives will build on 1) detailed study of virus biology and transmission under climate change conditions; 2) development of classical solutions (IPM and natural resistance) to control viral diseases with two distinct modes of transmission; 3) testing novel approaches (biopesticides, biological control, cross-protection) to mitigate viral diseases and to reduce pesticide usage. In order to take into account the diversity of vegetable cropping systems and viral diseases, focus groups involving extension services, commercial companies and growers will help co-designing research activities and mitigation strategies from the onset of the project.

NGS analysis pipelines are rapidly becoming part of the routine repertoire of research, clinical and public health laboratories in the public sector and private industry. Middle East Respiratory Syndrome-coronavirus (MERS-CoV) is only one example of the many recent virus discoveries made through analysis of next-generation sequencing (NGS) data. Yet, only a small part of the several millions of short-length sequence fragments generated by NGS machineries, many of which are expected to be of viral origin, can be analysed with current methods in bioinformatics. Even for well-known (pathogenic) viruses, proper epidemiological analyses are becoming more and more difficult due to the lack of bioinformatics tools that can handle the large and growing size of datasets. The VIROGENESIS consortium will overcome the most pressing bioinformatics obstacles to making full use of NGS by developing a software platform for end-users with tools underpinned by novel algorithms, models and bioinformatics methods. The speed and flexibility of the tools will make it possible to run analyses on a daily basis for a variety of subjects, including diagnostics, phylogeography, phylodynamics and transmission of drug resistance. The tools will be piloted and incorporated in the many available bioinformatics pipelines and software programmes used in the field. We will make our tools available in a modular, free and open source software platform that offers opportunities to SME’s to further exploit this market. The VIROGENESIS consortium brings together leading European academic and private small and medium enterprises (SME) bioinformatics developers and virology end-users who initiated this project in response to a clear interest from EMBL, NCBI and the Global Microbial Identifier (GMI) platform.