Population genetics and epidemiology

Many of our activities are located at the interface of epidemiology and population genetics. To fully understand the epidemiology of viral pathogens it is useful to study their population genetics, and how the micro-evolutionary process (or phylodynamics) that is driven by mutation dynamics within cells, is manifest at higher scales (individuals, groups, populations, and landscapes) after the influences of selection, recombination, and transmission have acted. 

Within the group, Roman Biek (rabies, ebola), Sarah Cleaveland (rabies), Dan Haydon (FMDV, rabies), and Richard Orton (FMDV with the Pirbright Institute) all have research interests that relate to this area. Rowland Kao has similar interests in using genetic markers in bovine Tb to inform the transmission dynamics of this bacterial pathogen. 

What we hope might be neutral genetic differences in pathogens are useful as tracers of pathogen movement, but non-neutral genetic differences are increasingly appreciated to play a critical role in transmission heterogeneity. Louise Matthews has general interests in how strain structure affects transmission dynamics, studying this in E. coli and Salmonella infections. Members of the group (Louise Matthews, Dom MellorDan Haydon) are also interested in the spread of antibiotic microbial resistance - and its potential exchange between human and livestock and wildlife populations, particularly Salmonella and Campybacter.  It is of course not only pathogens that are genetically diverse.  Host genetic variation is also a critical source of transmission heterogeneity, and this is an area research developed by Mike Stear and Louise Matthews (ovine nematodes), and Barbara Mable (effects of MHC on host-pathogen interactions).

The importance of population genetics is also manifest at smaller temporal and spatial scales.  We have particular interests in rapid within host evolutionary processes.  Members of the Centre work on the antigenic dynamics of trypanosome infections and the forces that drive the evolution of the architecture of the tryp VSG archive (Christina CobboldDan Haydon, Richard Reeve with Richard McCulloch and Liam Morrison in the Wellcome Centre for Molecular Parasitology); methods to compare the antigenic cross-reactivity of different viral capsids of the same viral species - essential to the design of viral vaccines for FMDV and Influenza (Richard ReeveDan Haydon); and the process of repeat mutation that relates to the timing and severity of myotonic dystrophy (Catherine HighamDarren MoncktonChristina Cobbold, and Dan Haydon).