Dissecting flavivirus pathogenesis in human brain at single-cell level

Project opportunity

This Earmarked Scholarship project is aligned with a recently awarded Category 1 research grant. It offers you the opportunity to work with leading researchers and contribute to large projects of national significance.

Neurotropic flaviviruses include important human pathogens such as West Nile (WNV), Japanese Encephalitis (JEV) and Zika virus (ZIKV). WNV and JEV can cause encephalitis in adults, while ZIKV infects foetal brain, causing microcephaly. Despite the medical importance of flaviviruses the molecular mechanisms that determine their neuropathogenesis are poorly understood due to (i) lack of the experimental models that recapitulate the cellular complexity of the brain and (ii) lack of the methods that allow in depth analysis of such systems until recently.

This project aims to understand how neurotropic flaviviruses infect human brain and cause neurological diseases. It will employ human brain organoids as a model of flavivirus infection in the brain to dissect the mechanisms of flavivirus neuropathogenesis in biologically relevant system. Organoids (also known as “brains in a dish”) will be infected with WNV, JEV and ZIKV and their transcriptomes will be analysed to reveal susceptibility of different cell types to infection and identify cell-specific virus-induced changes in gene expression in infected and bystander cells. Gathered data will be used to identify pathways and processes affected by the viruses in different cell types. The role of these pathways in viral pathogenesis will then be assessed via gene knock-down experiments. 

Working on this project the successful candidate will be a part of multi-disciplinary team of researchers that are the world leaders in molecular virology, stem cell technologies and systems biology. The project will provide the PhD candidate an opportunity to master the cutting-edge techniques such (e.g. single-cell and spatial transcriptomics, organoids technologies) as well as multiple methods of classical virology and molecular biology. The candidate will be based at a vibrant UQ St Lucia campus and will have access to state-of the-art UQ facilities as well as to the supportive and collaborative environment at the School of Chemistry and Molecular Bioscience.

Scholarship value

As a scholarship recipient, you'll receive: 

  • living stipend of $32,192 per annum tax free (2023 rate), indexed annually
  • tuition fees covered
  • single Overseas Student Health Cover (OSHC)


Dr Andrii Slonchak

School of Chemistry and Molecular Biosciences

Email: a.slonchak@uq.edu.au

Preferred educational background

Your application will be assessed on a competitive basis.

We take into account your

  • previous academic record
  • publication record
  • honours and awards
  • employment history.

A working knowledge of virology, molecular biology and innate immunity would be of benefit to someone working on this project.

The applicant will demonstrate academic achievement in the field(s) of virology, microbiology, molecular biology, biochemistry or related discipline and the potential for scholastic success.

A background or knowledge of genomics and bioinformatics is highly desirable.

Latest commencement date

If you are the successful candidate, you must commence by Research Quarter 1, 2024. You should apply at least 3 months prior to the research quarter commencement date.

If you are an international applicant, you may need to apply much earlier for visa requirements.

How to apply

You apply for this project as part of your PhD program application.

View application process