We are inviting applications for a Postdoctoral Research Scientist to work on the within-host evolutionary
dynamics, and transmission, of chronic viral infections (HIV and hepatitis C virus). You will join Dr Katrina
Lythgoe’s Evolution of Viral Infections Research Group, whose members collaborate closely with the
Pathogen Dynamics Research Group led by Professor Christophe Fraser.

We are looking for a Postdoctoral Research Scientist (or close to PhD submission) with strong quantitative
skills, with the specific aim of linking evolutionary processes that occur at the within-host and
epidemiological scales. Long-term chronic virus infections, such as HIV and Hepatitis C Virus (HCV), place
an enormous burden on global health. Viruses causing chronic infections are unique since their ability to
evolve rapidly combined with long durations of infection mean that virus evolution within individuals can
have a significant effect on the health of entire populations and regions, such as how quickly drug resistant
strains will spread, how virulence evolves, and how the virus adapts to the immunological background of
the host population. The aim of this project is to better understand how within-host evolutionary and
ecological processes affect viral evolution at the epidemiological scale.

The direction taken will depend on the strengths and interests of the successful candidate, but the overall
focus will be on analysing whole genome sequencing data to better understand the within-host evolution
and transmission of these viruses, including the roles of selection, recombination, and
compartmentalisation. The analysis may include both phylogenetic and population genetic approaches.
Existing primary data for this project includes whole-genome next generation HIV viral sequences from a
large number of longitudinally sampled individuals and transmission pairs. These sequences were
generated as part of the PANGEA consortium, with samples collected by the Partners in Prevention trial
team, and you will collaborate closely with the lead investigators. We will also be generating long-read
sequencing data from these and additional samples, and from longitudinally sampled HCV infected
individuals living in the UK, USA, and Brazil. This will provide an opportunity to work with extensive and
unique viral genetic data.