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 bul...
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ftunivsydney:oai:ses.library.usyd.edu.au:2123/21806 2023-05-15T13:53:25+02:00 Using Meta-Transcriptomics to Reveal the Diversity, Ecology and Evolution of Animal Viruses Harvey, Erin Elizabeth Hunter 2020-01-01 application/pdf https://hdl.handle.net/2123/21806 unknown The University of Sydney Faculty of Science, School of Life and Environmental Sciences https://hdl.handle.net/2123/21806 The author retains copyright of this thesis. It may only be used for the purposes of research and study. It must not be used for any other purposes and may not be transmitted or shared with others without prior permission. evolution virus virology metatranscriptomics Thesis Doctor of Philosophy 2020 ftunivsydney 2022-05-30T13:31:38Z 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. Thesis Antarc* Antarctic Antarctica The University of Sydney: Sydney eScholarship Repository Antarctic |
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evolution virus virology metatranscriptomics |
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evolution virus virology metatranscriptomics Harvey, Erin Elizabeth Hunter Using Meta-Transcriptomics to Reveal the Diversity, Ecology and Evolution of Animal Viruses |
topic_facet |
evolution virus virology metatranscriptomics |
description |
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. |
format |
Thesis |
author |
Harvey, Erin Elizabeth Hunter |
author_facet |
Harvey, Erin Elizabeth Hunter |
author_sort |
Harvey, Erin Elizabeth Hunter |
title |
Using Meta-Transcriptomics to Reveal the Diversity, Ecology and Evolution of Animal Viruses |
title_short |
Using Meta-Transcriptomics to Reveal the Diversity, Ecology and Evolution of Animal Viruses |
title_full |
Using Meta-Transcriptomics to Reveal the Diversity, Ecology and Evolution of Animal Viruses |
title_fullStr |
Using Meta-Transcriptomics to Reveal the Diversity, Ecology and Evolution of Animal Viruses |
title_full_unstemmed |
Using Meta-Transcriptomics to Reveal the Diversity, Ecology and Evolution of Animal Viruses |
title_sort |
using meta-transcriptomics to reveal the diversity, ecology and evolution of animal viruses |
publisher |
The University of Sydney |
publishDate |
2020 |
url |
https://hdl.handle.net/2123/21806 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_relation |
https://hdl.handle.net/2123/21806 |
op_rights |
The author retains copyright of this thesis. It may only be used for the purposes of research and study. It must not be used for any other purposes and may not be transmitted or shared with others without prior permission. |
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1766258516385857536 |