Environmental and applied virology: viruses, friends and foes

Holder: Assoc. Prof. Dr Jana Žel

Code: P4-0407

Duration: 1.1. 2019- 31.12.2024

The authors acknowledge the financial support from the Slovenian Research Agency (research core funding No. P4-0407).


With the program, we aim to obtain new knowledge and develop tools in the fields of:

a)    environmental virology

b)    virus inactivation

c)    biomedical production of viruses.

In the 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 the 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 the 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 cold plasma treatments as efficient and clean tools for virus disinfection purposes. 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 for all three fields 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 detection and accurate quantification of selected viruses, loop mediated isothermal amplification (LAMP) for field detection of potentially important viruses, and electron microscopy and infectivity assays for studying the viral integrity and infectivity, respectively.

Importance for the development of science

The program will influence scientific development in the virology field, especially in the environmental and applied virology. The increase of the knowledge on the fate of viruses in the environment will shed light on new viral transmission routes on plant and human hosts, which will open doors to new epidemiological studies. The strategies and pipelines for environmental sampling, sample processing and analysis that will be developed in this program will enable and encourage similar studies in other fields, extending the knowledge of environmental viruses behavior and impact to a global level. In addition, tools that will be developed to quantify (qPCR, ddPCR) or detect (qPCR, ddPCR, LAMP) selected viruses with predicted high impact on plant and human health, will serve to improve or establish new diagnostic procedures in other laboratories.

The outcomes of this program will surely be important to impulse both cavitation and plasma technologies as they will expand already growing application niches of both technologies and support investigations on the mechanisms of viral inactivation. Moreover, the results of the project will also be of high importance for water virologists, as they will offer new tools for inactivation of viruses in water, as well as for all scientists working in the water cleaning sector, offering an environmentally friendly, non-toxic substitution for other water decontamination methods.

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 and 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 have an important impact in this field, as it will surely be of help for future virus productions pipelines