At the beginning of 2024, the National Institute of Biology (NIB) obtained ISO/IEC 17025 accreditation for the end-to-end use of nanopore-based high-throughput sequencing (HTS) to detect quarantine viruses that can infect tomato, pepper, and cucurbits—viruses not yet present in the EU but capable of causing significant economic damage if introduced. This is the first accreditation of its kind globally, and our Microbiology Group (FITO) played a key role in achieving this milestone. The latest scientific results underpinning this achievement were published in the journals Microbiome and Water Research.
Event: “Insight into Plant Viromes—from Basic Research to State-of-the-Art Diagnostics” (Ljubljana, April 23, 2024)
NIB hosted a dedicated event showcasing HTS techniques as a revolution in virus detection and understanding. HTS enables non-targeted detection of known and previously unknown viruses, expanding knowledge of plant viromes (the community of all viruses in a sample). Because viruses lack universal conserved genes for targeted enrichment across the virome, random HTS approaches are essential: they sequence all nucleic acids (DNA, RNA) in a sample without prior expectations.
As emphasized by Assoc. Prof. Dr. Denis Kutnjak, head of the Microbiology unit at NIB, the adoption of HTS in the past 15 years has uncovered vast previously unknown viral diversity, often referred to as “viral dark matter.” At NIB’s Department of Biotechnology and Systems Biology, HTS has become indispensable—from pathogen discovery and diagnostics to gene expression studies in plant–microbe interactions, characterization of biopharmaceuticals (viral vectors and vaccines), and investigations of microbial evolution and diversity.
Nanopore Sequencing and Validation
Dr. Gerard Coyne (Oxford Nanopore Technologies) presented advances in nanopore sequencing, which reads DNA/RNA by measuring electrical signal changes as molecules pass through a membrane pore. The method enables rapid, cost-effective analysis, portable devices, and long-read sequencing—advantages over many established techniques.
In 2023, NIB validated the full workflow for nanopore HTS to detect quarantine viruses threatening tomato, pepper, and cucurbits, in accordance with EPPO (European and Mediterranean Plant Protection Organization) guidelines, using one virus as a validation case. In early 2024, NIB received ISO/IEC 17025 accreditation for this workflow. As noted by Assoc. Prof. Dr. Nataša Mehle, head of the national laboratory for plant virus, viroid, and phytoplasma diagnostics (also part of the EU Reference Laboratory at NIB), this represents a globally unprecedented accreditation type.
Research Foundations
The most extensive recent virome studies were conducted under the MSCA ITN INEXTVIR project (coordinated by NIB, with 15 partners from six EU countries), examining tomato viromes in crops, weeds, and nearby water bodies, and revealing numerous previously unknown viruses. Results were published in Microbiome and Water Research.
This achievement was also presented in the TV program Ljudje in Zemlja (https://www.rtvslo.si/rtv365/arhiv/175056520?s=tv).
