Revealing the evolution of freshwater fish viruses in the Murray-Darling Basin, Australia

Viruses account for the majority of emerging infectious diseases globally. Understanding how viruses establish infections in multiple hosts through a process called cross-species transmission is therefore central to our understanding of virus evolution and emergence. The advent of meta-transcriptomics opened up an alternative view of the vertebrate virosphere, showing that many host species harbour an abundance and diversity of viruses without causing disease. This is particularly true for fish, which have proven to serve as a rich source of virus diversity. Despite this, there is virtually no knowledge on the viruses that circulate in freshwater fishes across Australia, including those associated with biological invasions. The ongoing invasion of the common carp (Cyprinus carpio) in the Murray-Darling Basin has led to research into biological control measures, such as the use of cyprinid herpesvirus 3 (CyHV-3). The lack of described viruses in the Murray-Darling Basin raises questions regarding the safety of CyHV-3, as the consequences of cross-species transmission into native fishes are uncertain. In this thesis, I performed a meta-transcriptomic viral survey of invasive and native fishes across the Murray-Darling Basin. I identified 15 potentially novel viruses that could be assigned to 13 virus families. Notably, I revealed a marked lack of virus exchange between invasive and native fishes, particularly those viruses found in common carp. To my knowledge, this is the largest survey of freshwater fish viruses globally, covering over 2,200 km of the river system. The viruses identified in this thesis greatly facilitate biological control plans in Australia and enhances our understanding of the ecology and evolutionary history of vertebrate viruses more generally.