Investigating virus diversity in Australian domestic cats and bats

Abstract

The field of virus discovery has made dramatic advances since the development of metagenomic next-generation sequencing. Although this technique has been used to identify important novel viruses, to date there have been few studies using metagenomics to reveal the diversity and evolution of those viruses carried by wildlife and companion animal species in Australia. Similarly, the prevalence of enteric viruses in domestic cats is understudied in Australia compared to other countries. To reduce these major knowledge gaps, I used metagenomic next-generation sequencing to characterise the viruses present in five bat species (grey-headed, black and little red flying fox, large footed myotis and eastern-bent wing bat) and in faecal and tissue samples from healthy and diseased domestic cats. This led to the identification of 13 known viruses from the faeces of domestic cats and two from the tissue of bats. Additionally, sequence comparisons and phylogenetic analysis revealed eleven novel mammalian viruses from the families Astroviridae, Caliciviridae, Coronaviridae, Picornaviridae, Papillomaviridae and Retroviridae in domestic cat and bat faecal and tissue samples. By performing two large-scale domestic cat and grey-headed flying fox faecal virome studies, I also determined that a large diversity of viruses are shed via the faeces, including likely host, dietary, bacterial, fungal and invertebrate viruses. In addition, the studies presented in this thesis provide the first evidence of the circulation of feline kobuvirus, feline picornavirus, feline chaphamaparvovirus, bat sapovirus, bat astroviruses, bat kunsagivirus and possible exogenous bat betaretroviruses in Australia. In sum, this thesis presents an overview of the virus diversity in domestic cats and urban/suburban bat populations, highlighting the power of metagenomic sequencing to detect novel virus species in diseased and health mammals.