INEXTVIR · Project

Faster Plant Virus Detection Using Next-Gen Sequencing to Protect Crops

foodPrototypeTRL 4Thin data (2/5)

Imagine your crops are getting sick, but you can only test for diseases one at a time — like going to the doctor and running a separate blood test for every illness known to humanity. INEXTVIR trained a new generation of scientists to use advanced DNA-reading technology that scans for all plant viruses at once, like a full-body MRI for your field. They mapped the complete virus populations living in European agricultural crops and wild ecosystems, built bioinformatics tools to make sense of the massive data, and published standardized virome datasets online. The goal is to catch outbreaks faster, understand how viruses spread, and give regulators better data for decision-making.

By the numbers

consortium partners across multiple sectors

European countries covered

40%

industry participation ratio in consortium

SMEs involved in research and method development

project deliverables produced

The business problem

What needed solving

Plant viruses cause massive crop losses across Europe, but traditional diagnostic methods only test for one virus at a time — slow, expensive, and blind to unknown threats. Agricultural companies, seed producers, and regulators lack efficient tools to screen crops for the full spectrum of viruses circulating in their fields and ecosystems. Without comprehensive virome data, disease outbreaks catch the industry off guard.

The solution

What was built

The project produced validated NGS-based sequencing methods for plant virome analysis, bioinformatics tools for virus data classification and presentation, and standardized virome datasets published online covering multiple European crops. A total of 10 deliverables were completed, including the publicly available virome database in standardized tabular form.

Audience

Who needs this

Plant health diagnostic laboratories upgrading from single-target PCR to full virome screeningSeed companies needing comprehensive virus-free certification for planting materialNational plant protection organizations and phytosanitary regulatorsAgricultural biotech firms developing disease-resistant crop varietiesBioinformatics companies building crop disease surveillance platforms

Business applications

Who can put this to work

Agricultural Diagnostics

SME

Target: Plant health testing laboratories and diagnostic service providers

If you are a plant health lab still relying on single-target PCR tests for virus detection — this project developed and validated NGS-based sequencing methods that can detect all viruses in a crop sample at once. With 6 industry partners involved in method development and validation, the protocols were designed for transfer into routine diagnostic settings. This could dramatically reduce the number of tests you need to run per sample.

Seed Production & Crop Breeding

mid-size

Target: Seed companies and plant nurseries needing virus-free certification

If you are a seed producer dealing with the risk of distributing virus-infected planting material — this project built bioinformatics pipelines and standardized data formats for identifying viruses across multiple crop types. The virome datasets published online cover different crops from across Europe. This means you could screen mother plants more thoroughly before propagation, reducing costly recalls and crop failures downstream.

Agri-Tech Software

SME

Target: Bioinformatics and agricultural data analytics companies

If you are a software company building plant health monitoring tools — this project produced standardized virome data in tabular form published online, along with validated NGS data classification methods. With 15 consortium partners across 6 countries generating diverse crop virome data, the datasets and analytical methods could feed directly into your disease surveillance or risk prediction platforms.

Frequently asked

Quick answers

What would it cost to implement NGS-based virome screening in our lab?

The project data does not include specific pricing or cost-per-test figures. NGS sequencing costs have been dropping industry-wide, but implementation requires both equipment and bioinformatics expertise. Contact the consortium partners for specifics on validated protocols and their operational costs.

Can this scale to routine testing of thousands of crop samples per season?

The project specifically aimed to facilitate transfer and adoption of NGS methods into routine diagnostic settings. With 6 industry partners and 5 SMEs in the consortium, practical scalability was a design consideration. However, the project was primarily a training network, so full industrial-scale deployment would likely require further optimization.

Who owns the IP on the diagnostic methods and bioinformatics tools?

INEXTVIR was funded under MSCA-ITN, which is a training programme. The virome datasets were published openly online for the wider research community. IP arrangements for specific methods and tools would need to be discussed directly with the coordinator or relevant industry partners in the 15-member consortium.

Does this meet regulatory requirements for plant health certification?

The project explicitly aimed to enable informed risk assessment and decision making by regulatory communities. NGS method development and validation were core activities, designed to work within plant protection and diagnostic regulatory contexts. However, regulatory acceptance of NGS-based diagnostics varies by country and authority.

How long would it take to integrate these methods into our existing workflow?

The project ran from 2019 to 2023 and produced 10 deliverables including validated methods and standardized data formats. Integration timeline depends on your current lab setup and bioinformatics capacity. The standardized data formats were designed to facilitate adoption, but staff training in NGS analysis would be needed.

Can these tools detect viruses in any crop, or only specific ones?

The project studied virome across multiple agricultural crops and ecosystems across Europe, not just a single species. The bioinformatics methods and data classification tools are designed to work broadly. Specific crop coverage details would need to be confirmed with the consortium.

Consortium

Who built it

The INEXTVIR consortium is well-balanced for translating research into practice, with 15 partners split almost evenly between academia (6 universities, 2 research institutes) and industry (6 companies including 5 SMEs). The 40% industry ratio is unusually high for a training network and signals genuine commercial interest in the results. Partners span 6 countries (Belgium, Spain, France, Netherlands, Slovenia, UK), giving broad European coverage for virome data collection. The Slovenian national biology institute leads the coordination, which positions the project well for regulatory engagement. For a business looking to adopt these methods, the 5 SME partners are the most likely route to practical, commercially available tools and services.

NACIONALNI INSTITUT ZA BIOLOGIJOCoordinator · SI
UNIVERSITE DE LIEGEparticipant · BE
MEDNARODNA PODIPLOMSKA SOLA JOZEFA STEFANApartner · SI
ORGANISATION EUROPEENNE ET MEDITERRANEENNE POUR LA PROTECTION DES PLANTESpartner · FR
UNIVERSITY OF NEWCASTLE UPON TYNEparticipant · UK
UNIVERSIDAD DE MURCIApartner · ES
DELPHY BVpartner · NL
UNIVERSITE DE BORDEAUXparticipant · FR
BIOAZUL, SLpartner · ES
FERA SCIENCE LIMITEDparticipant · UK
INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENTparticipant · FR
UNIVERSIDAD POLITECNICA DE MADRIDparticipant · ES
BIOSISTEMIKA, RAZISKAVE IN RAZVOJ DOOparticipant · SI

How to reach the team

The coordinator is Nacionalni Institut za Biologijo in Slovenia. Use the CORDIS contact form or search for INEXTVIR project leads at NIB Slovenia.

Order a report on this consortium See NACIONALNI INSTITUT ZA BIOLOGIJO profile →

Next steps

Talk to the team behind this work.

Want to connect with the INEXTVIR team about licensing their diagnostic methods or virome datasets? SciTransfer can arrange an introduction and brief you on business-relevant results.

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