The Univeristy of Melbourne The Royal Melbourne Hopspital

A joint venture between The University of Melbourne and The Royal Melbourne Hospital

EDUCATION

Research Projects

Project: The space of evolutionary trees in infectious disease epidemiology

Davies Group

Infectious disease epidemiology largely relies on mathematical models that describe the epidemiological dynamics of such infectious diseases. These models typically consider the rate at which individuals are infected and recover from an infection. Because many infectious microbes, such as viruses and bacteria, evolve orders of magnitude faster than their hosts their genomes often have a signature of their transmission process. For example, HIV genome data are often used to infer the origin of outbreaks, the average number of secondary infections, and to detect superspreaders, a field known as phylodynamics. The crux of phylodynamics is that epidemiological processes have an expectation of the evolutionary relationships between pathogen samples. This project will pinpoint the key differences between evolutionary trees generated under different epidemiological processes.

This project has main aims; (i) estimating evolutionary parameters for a range of pathogens, such as HIV, influenza, and dengue, (ii) using these parameters to simulate evolutionary trees under different epidemiological models (e.g. susceptible-infected-recovered, SIS; susceptible-infected-recovered-susceptible, SIRS; and birth-death), and (ii) applying machine learning methods to identify whether epidemiological processes lead to a predictable patterns in evolutionary trees. The outcome of this project will be a framework to classify evolutionary trees from genome surveillance studies and will advance current efforts to couple genomics and epidemiology.

Contact project supervisor for further
information and application enquiries

Project Supervisor

Dr Sebastiane Duchene

Project availability
Master of Biomedical Science
Honours

Davies Group

mark.davies1@unimelb.edu.au

3 vacancies

Themes
Antimicrobial Resistance and Healthcare Associated Infections
Host Pathogens Interactions
Cross Cutting Disciplines
Discovery Research
Genomics
Indigenous Health
Public Health

The Davies group aims to apply genome sequencing methodologies and bioinformatics approaches to understand the evolution and transmission of bacterial pathogens. This knowledge can help facilitate a global understanding of pathogen evolution, in addition to informing public health intervention to reduce the disease burden associated with bacterial pathogens. Current projects address key research questions such as: is there a genetic difference between strains causing different disease manifestations? What is driving the emergence and dissemination of bacterial pathogens? Do host immune factors govern disease severity? Our research closely aligns with key international collaborators including the Wellcome Trust Sanger Institute in the United Kingdom.