The mission of the Institute for Emerging Infections is to understand the underlying processes that drive the emergence and spread of novel human infectious diseases. A multi-disciplinary team of biologists, mathematicians and clinicians are studying recently emerged infections and using the knowledge thus gained to anticipate challenges that will be posed by novel emergent infections in the 21st century.

A chance discovery has opened up a new method of finding unknown viruses.

Dr Aris Katzourakis, an Associate Professor, and Dr Amr Aswad, Research Associate at Oxford’s Department of Zoology, initially discovered the new use for the database, by chance. While looking for an ancient herpes virus in primates, they found evidence of two new undocumented viruses.

Spurred by their accidental discovery, they set out to see if they could intentionally achieve the same result. In a separate project to find new fish-infecting herpes viruses, they used the technique to examine more than 50 fish genomes for recognisable viral DNA. Sure enough, in addition to the herpes viruses they were expecting to find, the researchers identified a distant lineage of unusual viruses – that may even be a new viral family. The traits were found scattered in fragments of 15 different species of fish, including the Atlantic salmon and rainbow trout.

"The viral data collected, that may otherwise be discarded as a nuisance, is a unique resource for looking for both pathogenic and benign viruses that would otherwise have remained undiscovered."

Study author Dr Aris Katzourakis, from Oxford University’s Department of Zoology

Nature (2016)
Cartoon illustration of the drug concentration-dependent spatial model. (Nature 2016) See below.

A team of international researchers including scientists from Oxford University has found that HIV is still replicating in lymphoid tissue even when it is undetectable in the blood of patients on antiretroviral drugs.

The findings provide a critical new perspective on how HIV persists in the body despite potent antiretroviral therapy.

The study, led by Northwestern University, USA and University of Oxford, is published in the journal Nature.

“Deep sequencing is able to detect mutations in the virus that are present at very very low numbers,” says Helen Fryer. “We wanted to see if we could find mutational changes that are consistent with viruses going through cycles of replication. We know as HIV replicates, it makes mistakes pretty much every time it infects a new cell.”


Promoting discussion between HIV Specialists

Three members of the Institute for Emerging Infections have participated in the 23rd International HIV Dynamics and Evolution meeting. The three-day meeting was held in the Marine Biological Laboratory, set in Woods Hole, a beautiful coastal town in the southwest corner of Cape Cod.

This annual event aims to promote discussion on statistical, mathematical and computational approaches to analysing the dynamics and evolution of HIV-1. Themes that were covered in this years’ conference included viral reservoirs, drug resistance, within-host dynamics and epidemiology.

Professor Angela McLean, who is a member of the organizing committee, attended the meeting alongside Hannah Roberts and Dr Helen Fryer. Day one saw Hannah Roberts present a poster investigating why starting antiretroviral therapy in acutely infected patients leads to prolonged control after treatment interruption. On the final day of the meeting, Helen Fryer presented a new idea for HIV-clearance. She described how this idea was borne from her modelling work to characterise how persistent replication in drug sanctuaries could be topping up the HIV-1 reservoir in patients taking antiretroviral therapy. Both women received positive and constructive feedback on their work.

As well as being highly enjoyable and thought provoking, the event was a great opportunity to catch up with collaborators and past colleagues.

Human endogenous retrovirus (HERV) expression is not induced by treatment with the histone deacetylase (HDAC) inhibitors in cellular models of HIV-1 latency

While antiretroviral therapies have improved life expectancy and reduced viral loads in HIV-1-positive individuals, the cessation of treatment results in a rebound of viral replication. This suggests that a reservoir of latently-infected cells remains within these patients, the identity of which is ill-defined and therefore difficult to target therapeutically. Current strategies are aimed at using drugs such as histone deacetylase (HDAC) inhibitors to induce the expression of latent HIV-1 proviruses in order to activate and ultimately eradicate this reservoir of infected cells. One concern with the use of HDAC inhibitors is that they could up-regulate human endogenous retroviruses (HERVs), as well as HIV-1, with potentially pathophysiological consequences.


Hannah Roberts recently spent 3 months on a Research Councils UK policy internship, based at the National Assembly for Wales' Research Service. She was able to get involved in all aspects of the work of the Research Service's Health and Social Care team, which includes responding to regular enquiries from Assembly Members and writing proactive briefing papers on areas that are likely to be of interest to Members and relevant to the work of the Assembly. She very much enjoyed the experience and learnt a lot about writing in a clear, impartial and engaging manner, and about Welsh politics!


Daniel Wilson of the Oxford Martin School Programme on Curing Chronic Viral Infections has been awarded a prestigious Henry Dale Fellowship.

His project entitled "Statistical methods for whole genome phenotype mapping in bacterial populations" will address the question of how to detect genes or mutations in bacteria that increase the chances of causing severe infection.

The award consists of 5 years funding for Daniel and additional funds for a research assistant and associated lab costs.