Projects / Programmes source: ARIS

Environmental and applied virology: viruses, friends and foes

January 1, 2019 - December 31, 2027
Research activity

Code Science Field Subfield
4.06.00  Biotechnical sciences  Biotechnology   

Code Science Field
T490  Technological sciences  Biotechnology 

Code Science Field
4.04  Agricultural and Veterinary Sciences  Agricultural biotechnology 
Environmental virology, applicative virology, virome, virus inactivation, electron microscopy, digital PCR, high-throughput sequencing, absolute quantification, nucleic acids, virus concentration and purification, metagenome, viral vectors
Evaluation (rules)
source: COBISS
Data for the last 5 years (citations for the last 10 years) on April 14, 2024; A3 for period 2018-2022
Data for ARIS tenders ( 04.04.2019 – Programme tender , archive )
Database Linked records Citations Pure citations Average pure citations
WoS  339  10,846  9,600  28.32 
Scopus  336  12,220  10,869  32.35 
Researchers (19)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  29616  PhD David Dobnik  Biotechnology  Researcher  2019 - 2024  315 
2.  39127  PhD Ana Dolinar  Chemistry  Researcher  2023 - 2024  20 
3.  39118  PhD Arijana Filipić  Biotechnology  Researcher  2019 - 2024  84 
4.  27827  PhD Jon Gutierrez Aguirre  Biotechnology  Head  2019 - 2024  363 
5.  53538  Mojca Janc  Biotechnology  Junior researcher  2019 - 2024  16 
6.  58119  Amadej Jelenčič  Biology  Junior researcher  2023 - 2024 
7.  55808  Nina Kobe  Biotechnology  Junior researcher  2021 - 2024 
8.  25523  PhD Polona Kogovšek  Biology  Researcher  2019 - 2024  216 
9.  51291  Nejc Košir    Technical associate  2020 - 2021  15 
10.  35384  PhD Denis Kutnjak  Biotechnology  Researcher  2019 - 2024  288 
11.  55123  Živa Lengar    Technical associate  2021 - 2024  27 
12.  32501  PhD Tadeja Lukežič  Biotechnology  Researcher  2019 - 2022  54 
13.  51352  PhD Stephen Lewis Minger  Biotechnology  Technical associate  2019 - 2024  37 
14.  38081  PhD Anja Pecman  Biotechnology  Researcher  2019 - 2024  98 
15.  58118  Neža Praček  Biology  Junior researcher  2023 - 2024 
16.  30090  PhD Nina Prezelj  Biology  Researcher  2023 - 2024  61 
17.  09864  PhD Magda Tušek Žnidarič  Biology  Technical associate  2019 - 2024  414 
18.  56856  Lana Vogrinec  Biotechnology  Junior researcher  2022 - 2024  13 
19.  03765  PhD Jana Žel  Biotechnology  Former/secondary head  2019 - 2021  619 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0105  National Institute of Biology  Ljubljana  5055784  13,239 
Viruses are the most abundant biological entities in the biosphere and despite they are mostly known for detrimental effects on their hosts, recent research shows a spectrum of virus-host symbiotic relationships, including beneficial ones. They have an important role in evolution through gene transfer and recently they became high value tools in biomedicine and biotechnological fields. In the proposed program, we will study viruses from different points of view that focus both on their negative and positive attributes. We will address the composition of virome and fate of viruses in the environment, especially in different water samples, but also in soil and air. We will search for potential epidemiological impacts of underestimated virus transmission routes such as irrigation water, recycled wastewater, contaminated soil or particles in the air. We expect to gain new information on the impact of viruses in environment on plant and human health, and to offer methods to assess and predict that impact. Our preliminary data showed that some viruses remain infective outside hosts, in environmental waters, even after conventional wastewater treatment, thus, we will also test innovative and efficient technologies for waterborne virus inactivation. In collaboration with our established partners, we will evaluate the application of hydrodynamic cavitation and plasma treatments as efficient and clean tools for virus disinfection purposes. We will focus on the mechanisms of viral disruption using methods that enable characterisation of viruses at different levels: particle integrity, genome and infectivity. We expect to foster the technologies to reach a maximum virus inactivation efficiency and help with their future industrial application. With respect to the medical exploitation of viruses, we will apply all our expertise in virus purification, quantification and characterization to support the procedures for the production of viral vaccines and viral vectors for gene therapy. We will research and develop tools to improve critical steps of the virus production pipelines, such as proper separation and quantification of viruses, detection of contaminant nucleic acids, confirmation of the proper virus composition and conformation. This will result in an easier achievement of maximum yields and good quality viral products. Established analysis pipelines will combine state of the art methods. Monolithic chromatography for virus concentration, high-throughput sequencing to assess the metagenomic composition of samples, quantitative PCR and digital PCR for accurate quantification of selected viruses, loop mediated isothermal amplification for field detection of potentially important viruses, and electron microscopy and infectivity assays for studying the viral integrity and infectivity, respectively. The proposed program aims to obtain new knowledge and develop tools for the fields of environmental virology, virus inactivation and biomedical production of viruses.
Significance for science
The program will impulse scientific development in the virology field, especially in environmental virology and applied virology.   The increase on the knowledge of the fate of viruses in the environment will shed light on potentially new transmission route to plant and human hosts opening doors to new epidemiological studies. The metagenomics analysis of environmental samples implies the probable discovery of new viruses or other microbes with potentially important implications that will deserve further studies. The strategies and pipelines for environmental sampling, sample processing and analysis that will be developed in this program will also serve to impulse similar studies in other regions, extending in this way the knowledge on environmental viruses behavior and impact to a global level. In addition, tools that will be developed to quantify (qPCR, ddPCR) or detect (LAMP) selected viruses with predicted high impact on plant and human health, will serve to improve or stablish new diagnostic procedures for such viruses in other laboratories.   The outcomes of this project will surely be important to impulse both cavitation and plasma technologies as it will allow to expand their already growing application niches and support an increase in the investigations on the mechanisms of inactivation. Moreover, the results of the project will also be of high importance for water virologists, as it will offer new tools for inactivation of viruses in water, as well as for all scientists working on water cleaning, offering a environmentally friendly, non-toxic substitution for other water decontamination methods.The relevance of this research subject for the scientific field is strongly supported by our publication of the first evidence on virus inactivation by cavitation in the leading journal in the field of water research (Water research, A'') and the echoes and reactions generated in different scientific forums. Also, the ERC consolidation project that was recently granted to our collaborator at Faculty of mechanical engineering to study cavitation mechanisms is a good indicator of the relevance of our applicative project for the scientific field. Finally, the program will also contribute to the scientific field of viral vector production. By applying our expertise in virus separation, quantification and characterization, and in close collaboration with experts in the biomedicine field, such as Prof Stephen Minger, and with companies dealing with viral vaccines production, we expect to offer tools to assess and improve the quality and yields of virus production at different levels of the process. This will allow to impulse the field, as it will surely be of help for future virus productions pipelines.
Significance for the country
The results of our research, in particular the methodologies that will be developed, will definitely find their way to applications and to risk identification and management strategies by the public administration since the head and several researchers of the program, lead and carry out scientific advice for the Ministry of Agriculture, Food and Forestry, the Administration for Civil Protection and Rescue and the Ministry of the Environment and spatial planning and the Committee for the release of genetically modified organisms into the environment. They also participate in international bodies such as ENGL and EPPO, which will additionally help to promote Slovenian high-tech. Both in the analysis of air and environmental waters, we will discover a wide spectrum of microbes, among which they will also be pathogenic ones. Cooperation of program researchers with the Food Safety, Veterinary and Plant Health Administration, will ensure that they are quickly informed of any pathogen discovery so that they can begin to prepare methods for their diagnostics, to find the source of contamination and ultimately its elimination, which will contribute to prevent the health of plants, animals and human. The acquired knowledge and methodologies will be transmitted to the education system at various levels of higher education and doctoral education, as the head of the program is a habilitated professor at the University of Ljubljana and the International Postgraduate School Jozef Stefan. Education of young researchers on their way to a doctorate and master students will be also ensured through mentors of young reserachers. Due to the participation and leadership of program researchers in several international projects, the program will be strongly involved in international research trends including participation in European infrastructural projects.   Knowledge of what is happening in the environment is extremely important for planning interventions for its protection and cleaning. So far, the members of the program group have cooperated with the Central Wastewater Treatment Plant Domžale, which is the best-equipped and advanced such plant in Slovenia. They are extremely interested in what is happening with microbes after flowing through the treatment plant and what kind of microbial communities are found in environmental waters. In the field of concentration of viruses and nucleic acids from other microbes from the water, we will continue to use different methodologies, such as CIM chromatographic supports manufactured by the Slovenian high-tech company BiaSeparations, with which we will continue to impulse the use of their products for both environmental and clinical use. CIM chromatography is one of the most successful methods in the downstream purification process for viruses used for gene therapy or vaccines. By using the expertise gained in the program on viral purification, quantification and characterization, we will work closely with companies that deal with gene therapy and we will offer them tools for improving the quality and quantity of viral production at various levels through the production of gene therapy viruses and vaccines. This will enable a new impulse to this important, rapidly evolving field.
Most important scientific results Interim report
Most important socioeconomically and culturally relevant results Interim report
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