Periodic Reporting for period 2 - INEXTVIR (Innovative Network for Next Generation Training and Sequencing of Virome)
Reporting period: 2021-02-01 to 2023-07-31
Problem: Plant viruses cause 50% of the emerging plant diseases and pose an important threat to many agricultural crops worldwide. Whilst in developing countries they impact food security, in developed countries the impact is predominantly economic. Globally plant viruses are responsible for production losses estimated at €15 to 45 billion per year through lower yields and reduced product quality.
Opportunity: With the improvement in our ability to identify viruses has also come the recognition that not all viruses have a negative impact on their host. Increasing evidence suggests that some persistent virus infections can be beneficial or mutualistic to the infected plants (e.g. conferring tolerance to abiotic stresses). An improved knowledge of the plant virome will be of great interest to improve the sustainability of agricultural production and the resilience of crops to cope with both the long-term effects of climate change as well as the short-term effects of increasingly extreme weather patterns.
Overall objectives: INEXTVIR will provide information on the identity, diversity, ecology and biological impact of plant viruses in agricultural and natural ecosystems; enable the evaluation and interpretation of these findings and their potential impacts for stakeholders such as policy makers in plant protection, the agricultural sector or the society in general; and facilitate the transfer and adoption of new technologies and knowledge by end-users such as the phyto-diagnostics industry or plant health certification organizations.
Opportunity: With the improvement in our ability to identify viruses has also come the recognition that not all viruses have a negative impact on their host. Increasing evidence suggests that some persistent virus infections can be beneficial or mutualistic to the infected plants (e.g. conferring tolerance to abiotic stresses). An improved knowledge of the plant virome will be of great interest to improve the sustainability of agricultural production and the resilience of crops to cope with both the long-term effects of climate change as well as the short-term effects of increasingly extreme weather patterns.
Overall objectives: INEXTVIR will provide information on the identity, diversity, ecology and biological impact of plant viruses in agricultural and natural ecosystems; enable the evaluation and interpretation of these findings and their potential impacts for stakeholders such as policy makers in plant protection, the agricultural sector or the society in general; and facilitate the transfer and adoption of new technologies and knowledge by end-users such as the phyto-diagnostics industry or plant health certification organizations.
New results generated within the project enabled to raise the technological level of high throughput sequencing (HTS) use in plant virology and open new horizons for research is several directions. The results of the projects contributed to the establishment of guidelines for both, HTS use for plant virus diagnostics, including definition and establishment of procedure-specific controls (European plant protection organisation standard published) and also for virus characterisation (new version of guidelines published as a direct result of the project). Innovative tools have been developed enabling contamination monitoring in HTS experiments and one of the first implementations of deep learning for virus discovery. A huge amount of new plant virus discoveries within the project certainly represents a step beyond state of the art and also now enable both, opening of new research frontiers studying those viruses, as well as additional discoveries of novel viral agents, which were previously too divergent to be detected. Finally, new perspectives in virus ecology have been elucidated, e.g. by providing for the first time, clear examples on how water viromes can be used to increase the knowledge on plant virus presence and diversity in the ecosystem, which could be further employed for innovative approaches for virus surveillance in environment.
New virus findings, new diagnostic assays, frameworks and decision trees published during the project are being adopted by EU policy bodies such as European plant protection organization (a partner organization in the project) and transferred to the wider EU plant protection laboratories through European reference laboratories. The knowledge and expertise generated within the project on the detection of viruses in environmental water bodies (WP4) has been exploited to implement in Slovenia a nationwide SARS-CoV-2 monitoring in wastewater.
The project outcomes have been disseminated to scientific audience as well as to potential stake holders, through events such as:
- International Advances in plant virology conference in Ljubljana, co-organized by INEXTVIR consortium and the association of applied biologists, where all ESRs were able to present their results to the wider plant virology community.
-The organization of a hybrid round table on “Adoption and impact of high throughput sequencing in plant health: Seed testing, surveillance and certification” with presence of stake holders and experts.
-The organization of a satellite event in the frame of the 12th International congress of plant pathology in August 2023, in Lyon, France, where all INEXTVIR outcomes were presented to the largest gathering of plant pathology related experts and stake holders.
New virus findings, new diagnostic assays, frameworks and decision trees published during the project are being adopted by EU policy bodies such as European plant protection organization (a partner organization in the project) and transferred to the wider EU plant protection laboratories through European reference laboratories. The knowledge and expertise generated within the project on the detection of viruses in environmental water bodies (WP4) has been exploited to implement in Slovenia a nationwide SARS-CoV-2 monitoring in wastewater.
The project outcomes have been disseminated to scientific audience as well as to potential stake holders, through events such as:
- International Advances in plant virology conference in Ljubljana, co-organized by INEXTVIR consortium and the association of applied biologists, where all ESRs were able to present their results to the wider plant virology community.
-The organization of a hybrid round table on “Adoption and impact of high throughput sequencing in plant health: Seed testing, surveillance and certification” with presence of stake holders and experts.
-The organization of a satellite event in the frame of the 12th International congress of plant pathology in August 2023, in Lyon, France, where all INEXTVIR outcomes were presented to the largest gathering of plant pathology related experts and stake holders.
Progress beyond the state of the art:
•Setting up of an innovative holistic approach enabling the identification and characterisation of the virome of selected crops through an extensive sampling strategy and the cooperation of all project partners.
•Provision of an ecosystem perspective on the circulation of plant viruses in the environment by combining novel methodologies of sequencing environmental samples.
•Provision of an innovative framework to study virus epidemiology and emergence through the coupling of virome description with ecological and biological characterisation of new pathogenic and beneficial viruses.
•Development and validation of new NGS technologies for plant virome characterisation, including the bioinformatics solutions for big data analysis and transfer to routine diagnostics.
•Development of innovative approach integrating life and socio-economic sciences to build a bridge between scientific, industrial and regulatory stakeholders in plant pathology.
Expected results:
•ESR1: Investigation of the European field vegetable virome.
•ESR2: Virome characterization of European germplasm resources of pome fruits for future breeding and risk analysis
•ESR3: Survey and evaluation of the cultural practices impact on the virome of vegetable production systems and effect on sustainability.
•ESR4: Characterisation of tomato virome.
•ESR5: Research water as an important indicator of circulating plant viruses.
•ESR6: NGS-based viral indexing in Prunus species: virome characterization and validation of diagnostic approaches.
•ESR7: Ecological analysis of the plant virome structure and of reciprocal transfers between cultivated and wild host populations.
•ESR8: Effect of habitat biodiversity on the virome of wild plants and crops.
•ESR9: Effect of habitat biodiversity on virus host range evolution.
•ESR10: The cucurbits and lettuce virome.
•ESR11: Development and validation of innovative NGS tools for the fast and efficient detection of virus and virus-like agents in the selected crops.
•ESR12: Bioinformatics pipelines development for virome classification.
•ESR13: Development and integration of decision-making tools in data analysis procedures for NGS-based plant virus diagnostics.
•ESR14: Agronomic and socio-economic impact of virome.
•ESR15: Knowledge exchange platform.
•Setting up of an innovative holistic approach enabling the identification and characterisation of the virome of selected crops through an extensive sampling strategy and the cooperation of all project partners.
•Provision of an ecosystem perspective on the circulation of plant viruses in the environment by combining novel methodologies of sequencing environmental samples.
•Provision of an innovative framework to study virus epidemiology and emergence through the coupling of virome description with ecological and biological characterisation of new pathogenic and beneficial viruses.
•Development and validation of new NGS technologies for plant virome characterisation, including the bioinformatics solutions for big data analysis and transfer to routine diagnostics.
•Development of innovative approach integrating life and socio-economic sciences to build a bridge between scientific, industrial and regulatory stakeholders in plant pathology.
Expected results:
•ESR1: Investigation of the European field vegetable virome.
•ESR2: Virome characterization of European germplasm resources of pome fruits for future breeding and risk analysis
•ESR3: Survey and evaluation of the cultural practices impact on the virome of vegetable production systems and effect on sustainability.
•ESR4: Characterisation of tomato virome.
•ESR5: Research water as an important indicator of circulating plant viruses.
•ESR6: NGS-based viral indexing in Prunus species: virome characterization and validation of diagnostic approaches.
•ESR7: Ecological analysis of the plant virome structure and of reciprocal transfers between cultivated and wild host populations.
•ESR8: Effect of habitat biodiversity on the virome of wild plants and crops.
•ESR9: Effect of habitat biodiversity on virus host range evolution.
•ESR10: The cucurbits and lettuce virome.
•ESR11: Development and validation of innovative NGS tools for the fast and efficient detection of virus and virus-like agents in the selected crops.
•ESR12: Bioinformatics pipelines development for virome classification.
•ESR13: Development and integration of decision-making tools in data analysis procedures for NGS-based plant virus diagnostics.
•ESR14: Agronomic and socio-economic impact of virome.
•ESR15: Knowledge exchange platform.