Emerging viral diseases are posing an increasing threat to vegetable production worldwide. In Europe and beyond, two pathogens have become particularly concerning: Tomato brown rugose fruit virus (ToBRFV), which severely affects tomato crops, and Tomato leaf curl New Delhi virus (ToLCNDV), a whitefly-transmitted virus causing significant damage to cucurbits. As these diseases continue to spread across borders, sustainable management strategies have become essential for maintaining crop productivity and food security. To address this challenge, the Horizon 2020 VIRTIGATION project has brought together an international consortium of universities, research institutes, breeding companies, extension services and industry partners to develop innovative solutions for monitoring, understanding and managing these emerging viral diseases.
The project followed a comprehensive approach that combines scientific innovation with practical implementation. Its activities span six major objectives: engaging stakeholders in co-creating solutions, developing innovative diagnostic tools, improving our understanding of plant–virus– vector interactions, studying the impact of climate change on disease spread, implementing integrated virus and vector management strategies, and strengthening knowledge transfer throughout the agricultural value chain.
A defining feature of VIRTIGATION has been its strong emphasis on stakeholder engagement. During 2025, the consortium organised nine stakeholder events in English, French, Spanish, German and Dutch, bringing together more than 510 participants from across Europe. These events created opportunities for researchers, growers, advisers and industry representatives to exchange experiences, discuss practical challenges and identify priorities for future disease management.
Knowledge dissemination extended well beyond traditional meetings. A multilingual webinar series addressed topics such as integrated pest management, cross-protection using mild virus isolates, whitefly control, climate change and emerging virus threats (@virtigationproject on youtube). In addition, the project produced podcasts, videos and practice abstracts that reached thousands of viewers, ensuring that scientific results became accessible to growers and other stakeholders. The project's communication activities also achieved an international reach, with registered stakeholders representing 27 countries, demonstrating that the challenges addressed by VIRTIGATION are truly global.
One of the project's most significant scientific achievements has been the development of advanced virus sequencing technologies. Researchers established Oxford Nanopore long-read sequencing workflows capable of reconstructing complete viral genomes rapidly and at lower cost than conventional sequencing approaches. These methods provide substantially higher analytical throughput while allowing the detection of complete viral genomes, low-frequency variants and partial genomic components that are often missed by traditional diagnostics. Combined with the Genome Detective analytical platform (www.genomedetective.com), these technologies enable rapid phylogenetic classification of virus isolates and provide an unprecedented level of detail for monitoring virus evolution and disease outbreaks.
These innovative tools have already generated valuable insights into the epidemiology of both target viruses. For ToLCNDV, phylogenetic analyses showed that French virus populations most likely originated from Spain, supporting a south-to-north expansion along the Mediterranean coast. Furthermore, distinct genetic groupings among French isolates indicate that the virus entered France through multiple independent introduction events rather than a single invasion. Such information is essential for improving surveillance and preventing future outbreaks.
For ToBRFV, sequencing of virus populations collected in Belgium and France enabled researchers to reconstruct transmission pathways and monitor the spread of different viral lineages. Surprisingly, virus populations sampled from the same growers between 2021 and 2025 exhibited remarkable genetic stability. This finding suggests that current outbreaks are driven by stable virus populations that remain capable of overcoming resistance deployed in recently introduced tomato varieties, highlighting the need for continuous surveillance and the development of new resistance strategies.
Breeding resistant crop varieties remains one of the most sustainable approaches to disease control, and VIRTIGATION has made important progress in identifying new sources of resistance. Researchers discovered five wild tomato accessions exhibiting resistance to ToBRFV, including one accession with complete resistance. Genetic analyses linked resistance to the Nr1 locus, providing breeders with promising targets for developing more durable resistant tomato varieties.
The project also investigated resistance to the whitefly Bemisia tabaci, the insect vector responsible for transmitting ToLCNDV. Screening of more than one hundred cucumber accessions, combined with long-read sequencing and transcriptome analyses, identified structural variation associated with candidate resistance genes. These findings represent important steps toward reducing virus transmission through improved host resistance.
By integrating cutting-edge genomics, innovative diagnostics, epidemiological surveillance, resistance breeding and extensive stakeholder engagement, VIRTIGATION has established a strong foundation for sustainable management of emerging viral diseases. Beyond the scientific advances, the project has strengthened collaboration between researchers, industry and growers, ensuring that new knowledge can be rapidly translated into practical solutions. As viral diseases continue to threaten vegetable production under changing climatic conditions, the innovations and partnerships established through VIRTIGATION will contribute to more resilient and sustainable tomato and cucurbit production in Europe and beyond.