We are inviting applications for a Senior Postdoctoral Research Scientist to work on integrating the within-host and between-host evolution 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 Prof Christophe Fraser.

We are looking for a Senior Postdoctoral Research Scientist 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 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.