Chair and organiser
Professor Christophe Fraser, University of Oxford, UK
Epidemiology and population genetics of influenza in a tropical setting
Dr Maciej Boni, Oxford University Clinical Research Unit in Viet Nam, Vietnam
The epidemic dynamics and evolution of influenza A virus occur on a global scale. Influenza epidemics in temperate zones are seasonal and more predictable than transmission dynamics in tropical and sub-tropical areas, but the dynamics of these two climatic zones are closely linked, with East and Southeast (E/SE) Asia likely playing a major role in driving global influenza circulation. Influenza evolution affects the dynamics of influenza epidemics globally, but we do not know which human populations or which epidemiological conditions drive antigenic evolution in influenza. To answer this question would would need genetic and epidemiological data from regions of the world that are suspected to play a large role in global influenza dynamics. I will describe several such studies initiated in Vietnam that are aimed at understanding the circulation of human influenza viruses in Southeast Asia, as well as some of the new analytical methods we are developing to analyze the incoming data. Understanding Vietnam’s role in global influenza circulation will help us determine how important of a role E/SE Asia play in global flu dynamics, and it will help us identify which components of the Vietnam data would allow for similar analyses to be done in other Asian countries.
Phylogenomics and phylodynamics of Streptococcus pneumoniae
Professor William Hanage, Harvard School of Public Health, USA
The pneumococcus (Streptococcus pneumoniae) is a pathogen of global significance, for which effective vaccines are available against some serotypes. Molecular epidemiologic data, both genetic and genomic, have demonstrated that pneumococci experience a relatively high rate of recombination, which shuffles loci including resistance determinants among lineages and has generated vaccine escape genotypes. Effectively identifying those regions that have undergone recombination is a crucial step in the analysis of genomic data, such that genealogies may be constructed that are not distorted by horizontal gene transfer. It is essential that methods for identifying recombination work with emerging large genomic datasets, and ad hoc methods may be preferred in this context. The results also indicate that, as previously hypothesized, some pneumococcal lineages have experienced more recombination than others.
HIV as a model phylodynamic system
Dr Simon Frost, University of Cambridge, UK
Human immunodeficiency virus type 1 (HIV-1) is perhaps the most widely studied organism in viral phylodynamic studies, which aim to combine the epidemiology of viral transmission with the evolution of the virus, and for good reason. Not only is HIV-1 infection a significant public health issue, but a vast amount of sequence data has been generated over a period of decades, which when combined with the clock-like nature of HIV-1 evolution, allows fairly accurate reconstruction of past transmission events. Insights that have been gained by HIV-1 sequence analysis include identifying the timing of origin of HIV-1 epidemics, identifying period of exponential epidemic growth, and identification of 'transmission clusters' of infection. To date, rather simple models underlie the analysis of viral sequence data, which consider neither the detailed natural history of viral infection, nor the biased way in which sequence data is typically collected. Using HIV as an example of a model phylodynamic system, I will consider the importance of heterogeneity in geographic location, risk group, duration of infection, and age at infection in determining the structure of viral phylogenetic trees. I will also highlight how non-uniform sampling is an important confounding factor. [Joint work with Erik Volz].
The use of viral sequence data to evaluate the degree of disease superspreading, with an application to influenza H1N1pdm.
Professor Katia Koelle, Duke University, USA