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Viral evolution

Fundamental mechanisms of viral emergence and evolution
We perform in-depth studies of microbial emergence and evolution to determine the genetic and ecological factors that allow infectious agents (and other pathogens) to emerge and spread in populations.

Image courtesy of Ashley Gramza, Colorado State University

Our aims

Our objective is to develop an innovative and exciting research program that will put Australia at the forefront of research into emerging diseases, by establishing strong links with researchers throughout Australia and in the Asia-Pacific region, and by attracting top young scientists from diverse academic backgrounds to our research team.

Emerging infectious diseases are one of the great biomedical challenges of the 21st century. Environmental disruption, high population densities of humans, animals and crops, combined with global climate change, migration and rapid global transport networks are creating opportunities for pathogens to dramatically change their host range.

In our laboratory we perform in-depth studies of microbial emergence and evolution to determine the genetic and ecological factors that allow these infectious agents (and other pathogens) to emerge and spread in populations. Ultimately, we hope that this work will enable us to better prevent and control emerging diseases.

Although much of our work is directed toward understanding the fundamental mechanisms of viral emergence and evolution, we also consider a variety of other microbial pathogens and our research is both pure and applied. For example, we are involved in research investigating the use of viruses as biocontrol for European rabbits in Australia

Our research

Although we have broad interests in the emergence and evolution of infectious diseases our current research is centered around three main themes:

Understanding viral emergence

Much of our research is devoted to understanding the mechanisms by which viruses cross species boundaries and emerge in new hosts.

For example, why is it that influenza viruses are able to jump to humans from birds and pigs, and sometimes spread widely among us, while viruses like West Nile and hantaviruses seem unable to?

We are interested in determining why some types of virus seem intrinsically better able to cross species boundaries than others and the evolutionary determinants of this process. What are the microbial and host barriers involved?

Knowledge of this kind is essential because it will help us to predict, prevent, and control major disease epidemics in the future. As case studies we are employing a diverse range of human and animal viruses.

We are also interested in using evolutionary informed methods to control pathogens (‘evolutionarily informed disease intervention’) and encourage research projects in this area.

Comparative phylodynamics

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.

To understand the potential impact of emerging diseases on human and animal populations we aim to provide a quantitative understanding of the processes that determine the phylodynamic patterns of a wide range of viral infections. We are particularly interested in those viruses that pose a threat to health of the Australian population (such as dengue) or Australian animal species.

For example, how does the remarkable range of habitats and animal species in Australia shape patterns of disease transmission? We also aim to integrate evolutionary and epidemiological dynamics at the intra- and inter-host scales.

Evolution of Virulence

Although much of our work is directed toward understanding how viruses jump species boundaries, it is equally important to determine how a new virus will evolve after it has successfully emerged. Central to this is understanding the evolution of pathogen virulence.

We are interested in using comparative methods to reveal evolution of virulence determinants through time and the selection pressures acting on these sites.

In collaborations with researchers a CSIRO in Canberra we are studying the classic cases of two viruses used to control European rabbit populations in Australia – myxoma virus (MYXV) and rabbit haemorrhagic disease virus (RHDV).

Our people


For information about opportunities to work or collaborate with this group, contact Professor Edward Holmes via Research Supervisor Connect.


We have a well equipped bioinformatics laboratory, but can arrange for interested parties to perform laboratory work at the Westmead Millennium Institute, within the Charles Perkins Centre, and as part of the Marie Bashir Institute for Infectious Diseases and Biosecurity, or with our collaborators at other locations. There are also possibilities to spend time working in other laboratories abroad. Our major international collaborators include:

Edward Holmes

ARC Australian Laureate Fellow
  • Room 410 Biomedical Building C81