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Programmes Emerging Infections

Institute for Emerging Infections

The Challenge
New infections still present a threat to humanity. Novel pathogens often infect humans, but it is not yet well understood why only some pathogens acquire the ability to spread efficiently to other humans.

With greater insight into how chronic viral infections such as HIV, hepatitis C and influenza spread across populations, we can improve our progress in developing new and effective treatments to cure infectious disease. We aim to develop and implement strategies that tackle infections that persist in the host – often for a lifetime.

Our Approach
We combine the expertise of mathematicians and phylogeneticists who can manage huge amounts of data, with that of clinicians treating the affected individuals and laboratory scientists investigating disease pathogenesis. Bringing together these three groups of experts allows new questions to be tackled and, in particular, the development of new methods to make sense of the vast amounts of data produced with new experimental techniques.


John Frater’s group has identified biomarkers to help predict HIV positive patients who might be more ‘curable’, helping to shed light on the phenomenon known as ‘post-treatment control’, where the virus remains undetectable in some patients even after treatment is stopped. Professor Frater also receives support from the Oxford Martin School for his work on the HIV cure-targeting CHERUB collaboration between Oxford, Cambridge, Imperial, King’s College and UCL.

Ellie Barnes’ group is tackling issues around genetic variation of the hepatitis C virus, investigating the implications for how the virus develops and the potential for vaccines against it. They lead a national collaboration that has successfully developed high throughput HCV genomic sequencing, crossing traditional scientific boundaries with the integration of viral sequence data with host genetic analysis.

Investigating how host immune response controls complex pathogens, Paul Klenerman and his team are studying data derived from pandemic influenza, dengue and hepatitis C infection, using novel genomics technologies to probe the quality of immune responses.

The modelling and mathematical components led by Professor Angela McLean have brought unique insights and findings that would be otherwise impossible to disentangle. A recent study published in Nature shows convincing evidence that current HIV therapies may not block all HIV replication – as is the current but hotly contested dogma – but that there may be hidden sanctuaries of on-going virus production. These landmark data have major impacts for research strategy and the development of new interventions.

Oliver Pybus has developed new approaches to data interpretation that can analyse hundreds or thousands of viral sequences. Applications of these sort of approaches have allowed him to document the history of the HIV epidemic in central Africa and, more recently, to track the introduction and spread of Zika virus into the Americas.

Daniel Wilson and his group have developed new genetics methods that allow them to measure how infections are transmitted. For example, they have applied their methods to the Ebola virus (determining how it is transmitted between bats and humans), to drug-resistance in tuberculosis and to the outbreak of potentially lethal Klebsiella infections in neonatal units in Nepal.