Pathogen discovery and new perspectives on virus evolution
Access status:
USyd Access
Type
ThesisThesis type
Doctor of PhilosophyAuthor/s
Shi, MangAbstract
Viruses are ubiquitous, with a genetic and phenotypic diversity that surpasses any other group of organisms. Despite this, relatively little is known about the evolutionary history that has generated this remarkable diversity. The central aim of this thesis is to discover and ...
See moreViruses are ubiquitous, with a genetic and phenotypic diversity that surpasses any other group of organisms. Despite this, relatively little is known about the evolutionary history that has generated this remarkable diversity. The central aim of this thesis is to discover and document viruses in a broad spectrum of host species to better understand and characterize the key patterns and processes of virus evolution. With the help of next generation sequencing, I explored the viral content (virome) of more than 100 arthropod species. Strikingly, I discovered 128 novel viruses that appear to be ancestral to much of the documented genetic diversity of negative-sense RNA viruses and positive-sense RNA viruses of the family Flaviviridae. The wide diversity of viruses found in arthropods, as well as their deep phylogenetic positions, suggests that they represent an ancestral form from which viruses infecting vertebrates and plants evolved. Furthermore, I revealed a remarkable variation in genome structure, genome size, and replication/gene regulation strategies in these arthropod viruses, which in turn sheds important new light on the origin and evolution of virus genome organization. Hence, arthropods are a major reservoir of viral genetic diversity and have likely been central to viral evolution. As well as arthropods, I also performed virus discovery in vertebrates. Bats are a large group of mammals that harbor many zoonotic viruses. In this thesis, a systematic PCR screen of viruses was carried out on various species of bats collected at different locations in Kenya. This revealed enormous undocumented viral diversity in bats for both the Coronaviridae and Polyomaviridae families. Using bats as a model, I further studied the host and geographic associations of these viruses. I was able to show that genetic diversity in bats is primarily structured by host species and then by geographic distance. These data also suggest that virus transmission between distantly related hosts occurs occasionally during viral evolutionary history, although likely with a low rate of successful sustained infection in new host species. Overall, this thesis highlights the importance of a systematic pathogen discovery approach applied to a broad spectrum of hosts to reveal key aspects of virus origins and evolution.
See less
See moreViruses are ubiquitous, with a genetic and phenotypic diversity that surpasses any other group of organisms. Despite this, relatively little is known about the evolutionary history that has generated this remarkable diversity. The central aim of this thesis is to discover and document viruses in a broad spectrum of host species to better understand and characterize the key patterns and processes of virus evolution. With the help of next generation sequencing, I explored the viral content (virome) of more than 100 arthropod species. Strikingly, I discovered 128 novel viruses that appear to be ancestral to much of the documented genetic diversity of negative-sense RNA viruses and positive-sense RNA viruses of the family Flaviviridae. The wide diversity of viruses found in arthropods, as well as their deep phylogenetic positions, suggests that they represent an ancestral form from which viruses infecting vertebrates and plants evolved. Furthermore, I revealed a remarkable variation in genome structure, genome size, and replication/gene regulation strategies in these arthropod viruses, which in turn sheds important new light on the origin and evolution of virus genome organization. Hence, arthropods are a major reservoir of viral genetic diversity and have likely been central to viral evolution. As well as arthropods, I also performed virus discovery in vertebrates. Bats are a large group of mammals that harbor many zoonotic viruses. In this thesis, a systematic PCR screen of viruses was carried out on various species of bats collected at different locations in Kenya. This revealed enormous undocumented viral diversity in bats for both the Coronaviridae and Polyomaviridae families. Using bats as a model, I further studied the host and geographic associations of these viruses. I was able to show that genetic diversity in bats is primarily structured by host species and then by geographic distance. These data also suggest that virus transmission between distantly related hosts occurs occasionally during viral evolutionary history, although likely with a low rate of successful sustained infection in new host species. Overall, this thesis highlights the importance of a systematic pathogen discovery approach applied to a broad spectrum of hosts to reveal key aspects of virus origins and evolution.
See less
Date
2015-03-01Licence
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.Faculty/School
Faculty of ScienceAwarding institution
The University of SydneyShare