Comparative Viral Phylodynamics

Summary

• Phylodynamics.
• Comparative analysis of viral genome sequence data.
• Explaining successful cross-species transmission and emergence.

Supervisor(s)

Professor Edward Holmes

Research Location

School of Life and Environmental Sciences

Program Type

PHD

Synopsis

Phylodynamics is one of the most exciting new areas in evolutionary biology (and was in part developed by the supervisor).  The cornerstone of the phylodynamic approach is revealing link between epidemiological scale dynamics, such as patterns of disease incidence, and phylogenetic scale dynamics as manifest in the structure of phylogenetic trees.  Marrying these two scales can provide profound insights into infectious disease epidemiology.  

This project aims to understand the potential impact of emerging diseases on human and animal populations by providing a full quantitative understanding of the processes that determine the phylodynamic patterns of a wide range of viral infections.  Our key aim will be to determine which phylodynamic factors are most often associated with successful cross-species transmission, from which we will be able to predict the likely dynamics, patterns, and determinants of spread of any newly emerged virus, and in turn inform basic practice control strategies.  

We are particularly interested in those viruses that pose a threat to health of the Australian population (such as dengue and influenza) or Australian animal species.   For example, how does the remarkable range of habitats and animal species in Australia shape patterns of disease transmission?  We will therefore infer a number of key phylodynamic variables for a wide range of viral pathogens, including; (i) evolutionary rates, (ii) patterns and rates of population growth, (iii) patterns and rates of spatial spread, (iv) selection pressures, (v) recombination rates, (vi) host species and past history of cross-species transmission versus co-divergence, and (vii) key phenotypic features such as virulence, degree of antigenic variation, and associated clinical syndrome.  We will then categorise the range of phylodynamic patterns observed as well as their determinants, and identify those microbial groups, or types of phylodynamic pattern, that possess the characteristics that enable them to successfully jump species boundaries.

Additional Information

HDR Inherent Requirements

In addition to the academic requirements set out in the Science Postgraduate Handbook, you may be required to satisfy a number of inherent requirements to complete this degree. Example of inherent requirement may include:

- Confidential disclosure and registration of a disability that may hinder your performance in your degree;
- Confidential disclosure of a pre-existing or current medical condition that may hinder your performance in your degree (e.g. heart disease, pace-maker, significant immune suppression, diabetes, vertigo, etc.);
- Ability to perform independently and/or with minimal supervision;
- Ability to undertake certain physical tasks (e.g. heavy lifting);
- Ability to undertake observatory, sensory and communication tasks;
- Ability to spend time at remote sites (e.g. One Tree Island, Narrabri and Camden);
- Ability to work in confined spaces or at heights;
- Ability to operate heavy machinery (e.g. farming equipment);
- Hold or acquire an Australian driver’s licence;
- Hold a current scuba diving license;
- Hold a current Working with Children Check;
- Meet initial and ongoing immunisation requirements (e.g. Q-Fever, Vaccinia virus, Hepatitis, etc.)

You must consult with your nominated supervisor regarding any identified inherent requirements before completing your application.

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Keywords

Evolution, Phylodynamics, Australian Landscape, Emergence, Viruses, Comparative Analysis, Phylogeny, Dengue, influenza, adaptation

Opportunity ID

The opportunity ID for this research opportunity is: 1801

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