Exploring the diversity of CRESS DNA viruses associated with the faecal matter of wild and domestic animals in New Zealand.
Degree GrantorUniversity of Canterbury
Degree NameMaster of Science
Before the advent of cost-effective, efficient next-generation sequencing technologies, viral research predominantly focussed on viruses that were easily identified and those of importance to humans i.e. were pathogenic. Advances in viral metagenomic approaches in recent years have revolutionised the discovery of novel viruses. In particular, the number of described single-stranded DNA (ssDNA) viruses has grown rapidly. The increased rate of discovery revealed that ssDNA viruses a have higher abundance and diversity than previously thought. An increasing number of ssDNA viruses identified through metagenomic studies are too divergent to be classified into the current taxonomic system established by the International Committee on Taxonomy of Viruses and remain unclassified. Circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses have been identified in a variety of environmental samples using viral metagenomic approaches. A high number of CRESS DNA viruses are unclassified, prompting the proposal of new groupings, namely the gemycircularviruses, smacoviruses and cycloviruses. The studies that identified CRESS DNA viruses were largely conducted outside New Zealand up until 2013. New Zealand’s Gondwana ancestry and physical isolation provides a unique virome that has not been extensively explored. Further exploration of CRESS DNA viruses within New Zealand would shed light on the true diversity and prevalence of CRESS DNA viruses both within New Zealand and globally, and may provide support to proposed CRESS DNA virus groupings. Faecal sources harbour many potential host species and enable sampling of the virome of an ecosystem in a non-invasive manner. Accordingly, faecal sources have been used effectively to discover a wide variety of viruses in multiple studies. This dissertation utilised a viral metagenomic approach to identify CRESS DNA viruses in the faeces of wild and domestic animals sampled from sites across the South Island of New Zealand, expanding upon baseline data collected by other studies. Next-generation sequencing technologies were used to inform the design of specific abutting primers for the recovery of complete viral genomes from faecal matter. This approach recovered 38 complete CRESS DNA viral genomes and two circular molecules from 49 individual faecal samples. The recovered viruses were classified as gemycircularviruses (n=18), smacoviruses (n=12) or unclassified CRESS DNA viruses (n=8) according to BLASTx similarities in GenBank’s non-redundant database, genome-wide nucleotide pairwise identities and shared genome organisations with previously identified CRESS DNA viruses. The eighteen gemycircularvirus isolates represent eleven species, nine of which are novel, while the twelve smacoviruses constitute eleven species, including ten novel species. The remaining CRESS DNA viruses could not be classified and represent unique species. The CRESS DNA viruses identified in this study show a wide diversity and contribute significantly to our understanding of the prevalence and diversity of CRESS DNA viruses circulating within New Zealand.