ProfessorEdward Holmes

Project Opportunities

Title: The Evolution of Viral Emergence

Summary of opportunity:

• Understanding the evolutionary mechanisms by which viruses cross species boundaries and emerge in new hosts.
• Revealing the evolutionary and ecological determinants of viral emergence.
• Evolutionary (largely phylogenetic) analysis of viral gene sequence data.

Opportunity synopsis:

Determining the factors that allow some viruses to jump species boundaries and emerge in new hosts more readily than others is one of the key issues in the study of disease emergence.  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 Ebola or West Nile seem unable to?  Knowledge of this kind is essential because it will help us to predict, prevent, and control major disease epidemics in the future.   This project will use the evolutionary analysis of virus gene sequence data to investigate why some types of virus seem intrinsically better able to cross species boundaries than others and the evolutionary determinants of this process.  In particular, the project will examine the evolutionary and ecological factors that facilitate successful cross-species virus transmission.  As data sets the project will focus on a diverse range of human and animal viruses, including influenza viruses, hantaviruses and coronaviruses.

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Project Opportunities

Title: Genomics and the Evolution of Pathogen Virulence

Summary of opportunity:

• Evolution of pathogen virulence.
• Examining the evolution and spread of two viral agents of rabbit biocontrol in Australia – myxoma virus (MYXV) and rabbit haemorrhagic disease virus (RHDV).
• Comparative analysis.

Opportunity synopsis:

Although most studies of disease emergence have considered viruses and other pathogens 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.  In particular, will a pathogen evolve to become more or less nasty as it spreads in a new host?  Although there has been a great deal of theoretical work in this area, relatively little is known about the evolutionary genetic (genomic) basis to the evolution of pathogen virulence.  This project will utilize 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 the project will consider as the classic cases of two viruses used to control European rabbit populations in Australia – myxoma virus (MYXV) and rabbit haemorrhagic disease virus (RHDV).  This research may therefore also assist in the development of improved methods for biocontrol.

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Project Opportunities

Title: Exploring the Virosphere

Summary of opportunity:

The total universe of viruses - the virosphere - is vast but very poorly characterised, with more than 99.99% of viruses still to be discovered.  The goal of this project will be to use new metatranscriptomic techniques to describe some of this hidden virosphere, exploring what viruses lurk in a diverse range of bacteria, protozoa, and eukaryotes.

The student will be based at the Charles Perkins Centre for the duration of this project.

Opportunity synopsis:

To acheive this samples will be taken from diverse bacteria, protozoa, and eukaryote taxa and subjected to large-scale RNA-sequencing.  These sequence data will be subjected to extensive computational analysis.

----------Current Research Projects----------

• Revealing virus ecology.
• Exploring the virosphere (with 'meta-transcriptomics').
• The evolution of viral emergence.
• The evolution of virus virulence and host range.
• Studying microbial evolution and emergence using ancient pathogens.