Using Meta-Transcriptomics to Reveal the Diversity, Ecology and Evolution of Animal Viruses

Although viruses are ubiquitous, infecting all biological entities including viruses themselves, we know relatively little of viral diversity beyond those implicated in diseases affecting humans and domestic plants and animals. Recent advances in metagenomic sequencing technologies, particularly bulk RNA shotgun sequencing ('meta-transcriptomics'), have enabled a dramatic increase in our understanding of virus diversity and evolution. However, although likely central to disease emergence, the total viral diversity (i.e. virome) of many vertebrates and their eukaryotic parasites remain uncharacterised. In this thesis I use meta-transcriptomic based virus discovery to characterise both the viromes of species threatened by anthropocentric activities and their parasitic invertebrates. In total, I describe the discovery of 102 novel viruses in samples collected from four vertebrate species - eastern Australian Humpback whales, koalas and three species of Antarctic penguin. These viruses were often highly diverse from those previously characterised, providing a broadened perspective on virome diversity in these animals. In addition, due to their role as vectors of disease in humans and wildlife, ticks and fleas were collected during population studies of two species of eastern Australian Bandicoot as well as from Antarctic penguin nesting sites. Meta-transcriptomic analyses of these parasites identified 46 novel viruses, often highly divergent from those viruses previously characterised. Australia and Antarctica have unique fauna that have evolved in isolation for millions of years. It may therefore be assumed that the viruses infecting these species would be equally as divergent. Both Australian and Antarctic tick viruses clustered phylogenetically with other tick-associated viruses, suggesting that they co-evolved with their tick hosts as they have diversified