Virus Ecology and Evolution
To understand how viruses affect natural and agro‑ecosystems we investigate viral diversity, evolution and ecology using modern and classical virological tools, studying viromes of plants, animals (especially invertebrates) and environmental samples. We specialize in the use of shotgun high‑throughput sequencing and bioinformatics for plant virus discovery, detection and elucidation of experimental viral evolution and viral population dynamics.
In this research area, we have in recent years explored viral diversity across agroecosystems and surrounding weed communities, revealing extensive hidden plant virus diversity at the crop–wild plants interface. We have also characterized viromes in freshwater systems, including rivers and irrigation waters, demonstrating that environmental water captures rich viral signals from both natural and agricultural landscapes. Additionally, our work includes pioneering invertebrate virome studies in crayfish and investigations of viruses associated with microbes, such as phytoplankton. In parallel, we also study the stability, persistence, and spread of viruses in water, soil, and compost using controlled experimental approaches, helping us better understand how viruses move through and interact with different environments.
Environmental Virus Surveillance
For more than 20 years, we have been studying plant and mammalian viruses in diverse environmental samples: primarily water, but also soil, air, and other matrices such as glacier ice. At This expertise enabled us to rapidly establish Slovenia’s official SARS‑CoV‑2 wastewater monitoring system during at the onset of the COVID‑19 pandemic, providing a powerful tool for tracking viral circulation in the population. Building on this experience in virus concentration and environmental viromics, we are now investigating how virological surveillance of environmental water samples can support different epidemiological investigations, such as improving preparedness for the emergence of new viral strains (e.g., of avian influenza A virus) or enabling early detection of stable plant viruses that infect crops. In addition to surveillance, we also develop new approaches for virus removal from water, including hydrodynamic cavitation and cold plasma treatments, in close collaboration with mechanical engineers and physicists.
Plant virus and phytoplasma diagnostics
Our group conducts research and develops advanced, reliable methods for the detection of plant viruses, viroids, and phytoplasmas. Owing to our long-standing expertise, we have been designated as both a National and a European Reference Laboratory in this field. NIB leads the Slovenian National Reference Laboratory (NRL) for viruses, viroids, and phytoplasmas, coordinating a consortium with the Agricultural Institute of Slovenia and the Slovenian Institute of Hop Research and Brewing. As NRL, we provide validated diagnostics and expert support to national plant health authorities. At the European level, NIB is a designated partner in the EU Reference Laboratory (EURL) for viruses, viroids, and phytoplasmas, working in consortium with NVWA (Netherlands Food and Consumer Product Safety Authority, lead partner) and CREA (Council for Agricultural Research and Economics, Italy). Our main responsibilities are to support and advise NRLs across the EU, harmonize diagnostic standards, organize training and interlaboratory comparisons, and develop and validate advanced molecular methods for robust detection and management of these plant pathogens.
Phytoplasma Research
Our phytoplasma research aims to understand these tiny, wall-less bacteria that inhabit plants and insect vectors, causing serious diseases in crops. As they cannot be cultured in the laboratory, we study them directly in their natural hosts using advanced molecular and genomic techniques. We investigate how phytoplasmas spread between plants, their genetic diversity, and their interactions with insect vectors. Our work has identified new host plants, such as 16SrV phytoplasma on hazelnut, and invasive insects that may transmit these pathogens, including Flavescence dorée phytoplasma, a major threat to European vineyards. To better understand their biology, we have developed innovative methods to enrich and sequence phytoplasma DNA from field samples, enabling high-quality genome assemblies without the need for greenhouse propagation. By combining epidemiology, genetics, and advanced sequencing technologies, we aim to improve diagnostics, monitor disease outbreaks, and support sustainable management of phytoplasma-related threats to agriculture.
Antiviral Substances and Materials
With start of COVID-19 pandemics we started to support research and development of new materials with antiviral activity. We set up a system for testing the filtration efficiency of medicinal face masks. The system was developed for bacteria and viruses (bacteriophages). We developed also protocols for evaluation of antiviral activity, on model bacteriophages, of different functionalized materials for masks (e.g. textile with copper and graphene) and surfaces. We established also system with mammalian cell cultures and model viruses. We focus on respiratory viruses (adenovirus, coronavirus, influenza) and gastroenteric viruses (norovirus). Our aim is to explore antiviral properties of various chemicals, natural compounds and plant extracts. Here we combine computer power (in silico search) with in vitro assays (plaques assay, TCID50), molecular biology approaches and microscopy techniques (light, electron) to evaluate the antiviral activity of the compounds and elucidate the mechanisms of action of the lead compounds.