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Development and employment of untargeted and targeted tools for virus detection in the frame of water-based epidemiology

Author(s): Olivera Maksimović (Author), Jon Gutiérrez-Aguirre (Supervisor), Denis Kutnjak (Co-Supervisor)

Year: 2023

Type: Doctoral dissertation

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 …

Diversity of viruses infecting tomato and weed plants in agroecosystems

Author(s): Mark Paul Selda Rivarez (Author), Denis Kutnjak (Supervisor), Maja Ravnikar (Co-Supervisor)

Year: 2022

Type: Doctoral dissertation

Viruses, satellite viruses, viroids, virusoids, and satellite nucleic acids (herewith, referred to collectively or in part as ‘viruses’) comprise the virosphere and are perhaps the most diverse and abundant, yet still under-sampled, microbes on Earth. They are primarily regarded as pathogens or parasites of their eukaryotic or prokaryotic hosts. In …

The use of high-throughput sequencing for detection of viral sequences in complex samples from environment and industry

Author(s): Katarina Bačnik (Author), Maja Ravnikar (Supervisor), Denis Kutnjak (Co-Supervisor)

Year: 2022

Type: Doctoral dissertation

Metagenomics based on high throughput sequencing (HTS) has opened a new era of discovery and genomic characterization of viruses associated with a given host or environment. The search for novel viral sequences provides an excellent opportunity to improve early detection of pathogens, and to predict viral hosts and environmental reservoirs …