Project title: Mechanistic modelling to understand epidemic dynamics of vector-borne zoonotic diseases in Australia

Multiple vector-borne zoonotic pathogens cause disease and death in humans and livestock in Australia, including Murray Valley (MVEV), Kunjin (KUNV), and Japanese encephalitis (JEV) viruses. These three flaviviruses exhibit complex transmission cycles between multiple non-human hosts (e.g. ardeid birds, swine) and mosquito vector species; spillover infections in humans cause encephalitis disease, which can result in serious and fatal illness. MVEV and KUNV are both endemic to northern regions of Western Australia and the Northern Territory, with JEV also likely established in these regions following its unprecedented incursion into Australia in 2021.

JEV had previously only been sporadically detected in Australia's tropical northern extreme in the Torres Strait, but in early 2022 infections were detected in the temperate southern states of Victoria and South Australia. By the end of autumn 2022, JEV had resulted in seven confirmed human deaths and livestock loss in many commercial piggeries. During the 20th century there were several outbreaks of MVEV on the east coast of Australia but from 1975–2010 MVEV was almost entirely confined to endemic and adjacent areas. In 2011 MVEV cases were detected across Australia (except Victoria), and in 2023 MVEV cases were detected in South-Eastern Australian states including the first confirmed cases in Victoria since 1974. Despite seemingly ideal conditions for transmission of MVEV, there were only two detections of JEV in humans in the summer of 2022–2023 and no detections in humans in the summer of 2023–2024. Factors driving these sporadic outbreaks in Australia are poorly understood, hampering government efforts to anticipate and respond.

This PhD project will develop mechanistic models of transmission dynamics for vector-borne zoonotic pathogens with multiple host species. Mathematical analysis and simulation-based approaches will be used to assess potential mechanisms driving outbreaks and multi-year epidemic dynamics of MVEV, JEV, and KUNV in Australia, including:
A. Migration of wildlife host species (e.g. waterbirds) from endemic to non-endemic areas.
B. The buildup of wildlife host species immunity during epidemic years.
C. Climatic events impacting mosquito population dynamics.
D. The role of an amplifying host species at high density (e.g. domestic pig farming).
The results of these mathematical analyses will be used to develop recommendations on ecological and epidemiological surveillance studies that should be prioritised to improve understanding of flavivirus transmission dynamics in Australia.

The PhD student will be a member of Melbourne Mathematical Biology based in the School of Mathematics and Statistics, and the Infectious Disease Dynamics Unit at the Centre for Epidemiology and Biostatistics at the University of Melbourne (Parkville Campus). The project will be supervised by Dr Oliver Eales, A/Prof Freya Shearer, and Dr Marya Potorek.

Essential criteria

• Meets the University of Melbourne’s entry requirements for a Doctor of Philosophy (PhD) in Science. https://study.unimelb.edu.au/find/courses/graduate/doctor-of-philosophy-science/entry-requirements/
• A master's degree or four-year bachelor's degree with first-class honours in mathematics, statistics, biostatistics, biology, epidemiology, physics, computer science, or equivalent STEM subject area with demonstrated quantitative skills, including experience with ordinary differential equations.
• Some experience in programming (e.g., R or python).
• Able to meet the University of Melbourne’s Graduate English Language requirements. https://study.unimelb.edu.au/how-to-apply/english-language-requirements/graduate-english-language-requirements

Desirable criteria

• Demonstrated experience in the mathematical modelling of infectious diseases, or related methods (e.g. dynamical systems, stochastic processes, computational methods).
• Demonstrated experience with statistical modelling and Bayesian inference.

How to apply

Interested candidates who satisfy the essential criteria should apply by emailing {oliver.eales@unimelb.edu.au} with a single pdf file attached that contains the following:

• A maximum one page cover letter that outlines your interest in your project, your skills and experience, and how you meet the selection criteria.
• A formal transcript of your academic record from your university that details the subjects taken, the grades you received, and what the grading scheme means if it is not obvious. Transcripts should be translated into English, if applicable. You should include a transcript for all relevant degrees (i.e., if you have both a bachelors and a masters degree, include a transcript for both).
• A brief CV.

Applications will be assessed on an ongoing basis until 21 August 2026, with shortlisted candidates invited for a brief discussion over Zoom.

The successful applicant will apply for admission and a scholarship through the regular University of Melbourne graduate research admission and scholarship round supported by the supervision team, in September 2026. If the applicant were successful, the scholarship would cover tuition, a living allowance of AU$39,500 per annum, and a relocation grant of AU$2000 (interstate) or AU$3000 (international).

https://study.unimelb.edu.au/find/courses/graduate/doctor-of-philosophy-science/