Coalescent inference for infectious disease

Today my student Bethany Dearlove has her first paper published, called Coalescent inference for infectious disease: meta-analysis of hepatitis C. In this paper, published in Philosophical Transactions of the Royal Society B, we have developed coalescent-based population genetics methods for popular, deterministic, epidemiological models known as SI (susceptible-infectious), SIS (susceptible-infectious-susceptible) and SIR (susceptible-infectious-recovered). By implementing these methods in BEAST, we were able to re-analyse previously published hepatitis C virus datasets and directly estimate epidemiological parameters. Our results show that, in the absence of co-infection, the widely-used exponential growth and logistic growth models of changing population size correspond directly to SI and SIS dynamics. We were also able to examine the limitations to genetic approaches to reconstructing epidemiological dynamics.

This paper appears as part of an issue on Next-generation molecular and evolutionary epidemiology of infectious disease, which accompanies a Royal Society discussion meeting organized by Oli Pybus, Christophe Fraser and Andrew Rambaut. The Royal Society has made audio recordings of the talks at this meeting, and the accompanying satellite meeting, available online, including my talk on Bethany's paper.

Evolutionary Genetics for Translational Research

This month saw the 2010 Infectious Disease Genomics & Global Health meeting at Hinxton, which attracted a good number of people involved in the Modernising Medical Microbiology consortium, of which I am a participant. Rory Bowden and Rosalind Harding presented our group's progress on piecing together intra-host evolution of Staphylococcus aureus and reconstructing transmission chains in Clostridium difficile. My role in the projects has so far been one of assisting in ongoing evolutionary analyses and collaborating in the design of bioinformatics pipelines to make sense of the raw Illumina short-read sequencing data. At the same time I have been devising research plans for my own group, and spending time in the lab preparing sequencing experiments with Bernadette Young. In the poster I presented at Hinxton (available here), and at an internal talk I gave earlier in the year (slides here) I set out what I see as the strengths of Evolutionary Genetics for addressing translational medical problems including

• Tracking the transmission of hospital-acquired pathogens
• Understanding transmission dynamics at the population level
• Identifying the mechanistic and adaptive basis of disease
• Explaining how pathogens emerge, persist and spread globally

Of the many stimulating talks at the Hinxton conference, those by Dominic Kwiatkowski on the population genomics of Plasmodium falciparum, Christophe Fraser on "hyper-recombination" in Streptococcus pneumoniae and Paul Keim on the challenges for understanding the population genetics of non-clonal bacterial pathogens particularly interested me. Prof Keim gave an equally captivating talk the following day at the Health Protection 2010 meeting in Warwick on his microbial forensics work tracing the origin of Bacillus anthracis spores used in bioterrorism attacks. What I especially admired about his presentations was the dogged pursuit of new methods and ways of thinking in order to better address the biological questions at hand.