| Title: | Development and employment of untargeted and targeted tools for virus detection in the frame of water-based epidemiology : doctoral dissertation |
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| Authors: | ID Maksimović, Olivera (Author)
ID Gutiérrez-Aguirre, Ion (Mentor) More about this mentor... 
ID Kutnjak, Denis (Comentor) |
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| Files: |  DR_Maksimovic_Olivera_2023.pdf (39,42 MB)
MD5: 027F8B34DDFD172A68E819732DC0F5E6
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| Language: | English |
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| Work type: | Doctoral dissertation |
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| Typology: | 2.08 - Doctoral Dissertation |
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| Organization: | MPŠ - Jožef Stefan International Postgraduate School
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| Abstract: | 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. |
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| Keywords: | high-throughput sequencing, water-based epidemiology, viruses, doctoral dissertation |
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| Place of publishing: | Ljubljana |
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| Place of performance: | Ljubljana |
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| Publisher: | O. Maksimović |
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| Year of publishing: | 2023 |
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| Year of performance: | 2023 |
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| Number of pages: | XXIII, 91 str. |
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| PID: | 20.500.12556/ReVIS-13744 |
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| COBISS.SI-ID: | 168261635 |
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| UDC: | 579.68:578(043.3) |
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| Note: | Besedilo v angl.;
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| Publication date in ReVIS: | 23.04.2026 |
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| Views: | 97 |
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| Downloads: | 2 |
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