Identification of CRESS DNA viruses in faeces of Pacific flying foxes in the Tongan archipelago
Thesis DisciplineBiological Sciences
Degree GrantorUniversity of Canterbury
Degree NameMaster of Science
Viruses with circular single-stranded DNA (ssDNA) genomes are the smallest pathogens known to infect various organisms. Due to advances in high-throughput sequencing technologies, the diversity of circular replication associated protein encoding single-stranded (CRESS) DNA viruses is beginning to unravel. Viral metagenomic studies have demonstrated that animal faecal matter harbours a high viral diversity and therefore can potentially be used to explore viruses within ecosystems. Faecal matter may contain viruses shed by the infected animal or those that are associated with its diet and the environment. Besides capturing the viral diversity, faecal sampling is a non-invasive to the animal hence can be used easily for viral surveillance in ecosystems. A limited amount of work has been done on CRESS DNA viruses circulating in the Pacific Islands of Tonga. Prior to this study, only six species of CRESS DNA viruses had been identified. As part of a continuing effort to determine the diversity of CRESS DNA viruses, I sampled Pteropus tonganus faeces. P. tonganus, also known as the Pacific flying fox, is the most widespread bat species in the Pacific and is the only bat species found in the Tongan archipelago. Pacific flying foxes roost in trees and are frugivores. This thesis research was carried out to identify CRESS DNA viruses that are associated with Pacific flying fox faeces in Tonga. Faecal samples were collected from four P. tonganus roosting sites (Ha’ateiho (‘Atele), Lapaha (Takuilau), Ha’avakatolo and Kolovai) located in Tongatapu the main island of Tonga in 2014 and 2015. A next-generation sequencing informed approach was used to recover complete CRESS DNA viral genomes. In total, five novel cycloviruses (three species), 25 novel gemycircularviruses (13 species), 17 unclassified novel CRESS DNA viruses (15 species), a putative multicomponent virus (three cognate molecules) and two circular DNA molecules, were recovered. A number of viruses were identified in more than one sampling site in Tonga, suggesting these viruses have a broad distribution across the island amongst the Pacific flying fox colonies. Several species were identified in both 2014 and 2015 suggesting these viruses are persistently associated with faecal matter of Pacific flying foxes. The data obtained from this study has significantly expanded the knowledge of CRESS DNA viruses that are circulating in Tonga.