20.500.12556/ReVIS-13744 Development and employment of untargeted and targeted tools for virus detection in the frame of water-based epidemiology doctoral dissertation Razvoj in uporaba netarčnih in tarčnih orodij za zaznavanje virusov v okviru epidemiologije voda Traditional methods of studying viruses are limited in their ability to detect novel pathogens, but recent advances in high-throughput sequencing (HTS) are changing that. HTS allows researchers to probe deeply into the virome of various hosts and environments, identifying known and unknown viral species. However, a targeted approach, like quantitative PCR, remains the golden standard for large-scale quantitative studies. The increasing popularity of water-based epidemiology (WBE) to monitor wastewater for pathogens has become particularly widespread with surveillance of SARS-CoV-2 during the COVID-19 pandemic. Optimizing this procedure demands an evaluation of the stability of the virus in wastewater and a suitable concentration method for improving detection sensitivity. Real-time quantitative reverse transcription PCR (RT-qPCR) is the primary method used for detecting SARS-CoV-2, and validation of assays using appropriate reference materials and matrices is crucial. Plant viruses present similar challenges, with tomato brown rugose fruit virus (ToBRFV) being highly stable and potentially infectious for extended periods in water. Detection of ToBRFV in Slovenian wastewater before detection in plant samples raises concerns about the virus’ s origin, undetected presence, waterborne transmission risks, and using such water sources for agricultural irrigation during water scarcity. Simple and effective methods for ToBRFV concentration and detection from water samples are essential to analyze potential release from infected plants into water sources. Metagenomics analysis of environmental water used in irrigation can provide insight into the types of viruses to which plants are exposed, shedding light on virus transmission dynamics in agricultural settings and aiding in developing effective management strategies. It is a valuable tool for detecting known and unknown viral species in the ecosystem under investigation, providing an early warning system to prevent potential outbreaks. By applying knowledge and techniques from wastewater monitoring for human pathogens, it may be possible to detect plant viruses in irrigation water. In conclusion, advances in HTS-based metagenomics research and WBE can revolutionize virus detection and surveillance in human and plant systems. Tradicionalne metode preučevanja virusov so omejene pri odkrivanju novih patogenov, vendar nedavni napredek na področju visoko zmogljivega sekvenciranja (HTS) to spreminja. Uporaba HTS omogoča poglobljeno analiyo viromov različnih gostiteljev in okolij ter odkrivanje znanih in neznanih vrst virusov. Kljub temu tarčni pristopi, kot je kvantitativna PCR, ostajajo zlati standard za obsežnejše študije. Uporabnost študij epidemiologije na osnovi vode (water-based epidemiology, WBE) za spremljanje patogenov v odpadnih vodah se je globalno razširila, med pandemijo COVID-19, ko se je spremljalo širenje SARS-CoV-2. Optimizacija takšnega postopka zahteva oceno stabilnosti virusa v odpadni vodi in ustrezno metodo koncentracije za izboljšanje občutljivosti detekcije. Kvantitativni PCR v realnem času z reverzno transkripcijo (real-time quantitative reverse transcription PCR) (RT-qPCR) je osnovna metoda, ki se uporablja za odkrivanje SARS-CoV-2, pri čemer je ključnega pomena validacija testov z uporabo ustreznih referenčnih materialov in matric. Rastlinski virusi predstavljajo podobne izzive, zlasti virus rjave grbančavosti plodov paradižnika (ToBRFV), ki je v vodi zelo stabilen in potencialno kužen dlje časa. Zaradi odkritja virusa ToBRFV v odpadni vodi nekaj let pred njegovim odkritjem v rastlinskih vzorcih, se zastavljajo vprašanja o izvoru virusa, njegovi nezaznavni prisotnosti, tveganju prenosa z vodo in uporabi takšnih vodnih virov za namakanje v. Enostavne in učinkovite metode za koncentracijo in odkrivanje virusa ToBRFV v vzorcih vode so ključne za odkrivanje morebitnega sproščanja virusov iz okuženih rastlin v vodne vire. Analiza metagenoma okoljske vode, ki se uporablja za namakanje, omogoča vpogled v vrste virusov, ki so jim rastline izpostavljene. To prispeva k razumevanju dinamike prenosa virusov v kmetijskem okolju in pomaga pri razvoju učinkovitih strategij zaščite rastlin. Metoda omogoča vzpostavitev sistema zgodnjega opozarjanja in s tem preprečevanje morebitnih izbruhov, in je pomembno orodje za pravočasno odkrivanje znanih in neznanih vrst virusov v preiskovanem ekosistemu. Uporaba znanja in tehnik nadzora humanih patogenov v odpadnih vodah omogoča tudi odkrivanje rastlinskih virusov v namakalni vodi. Za zaključek lahko povzamemo, da napredek pri raziskavah metagenoma s HTS in WBE prinaša revolucionarne izboljšave pri odkrivanju in nadzoru virusov pomembnih za človeka in rastline. high-throughput sequencing water-based epidemiology viruses doctoral dissertation epidemije odpadne vode visoko zmogljivo sekvenciranje true false false O. Maksimović Angleški jezik Slovenski jezik Doktorsko delo/naloga 2026-04-23 10:32:28 2026-04-23 10:32:29 2026-04-26 03:15:45 0000-00-00 00:00:00 2023 0 Ljubljana 2023 Ljubljana Besedilo v angl.; XXIII, 91 str. 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 579.68:578(043.3) 168261635 DR_Maksimovic_Olivera_2023.pdf DR_Maksimovic_Olivera_2023.pdf 1 027F8B34DDFD172A68E819732DC0F5E6 2d7afe3f50ea4e945a37ccfd14614b548bdcb32863574de33a06fa60ae87aafe b45d4c9f-3f0f-11f1-b867-001a4af901a5 https://revis.openscience.si/Dokument.php?lang=slv&id=16608 Mednarodna podiplomska šola Jožefa Stefana 0 0 0