Chair
Professor Andrew Rambaut University of Edinburgh UK
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Professor Andrew Rambaut University of Edinburgh UK
Professor Andrew Rambaut University of Edinburgh UK
Andrew Rambaut is Professor of Molecular Evolution at the Institute of Evolutionary Biology, University of Edinburgh, where he also studied as an undergraduate. He received his DPhil from the University of Oxford in 1997. His research is centred on the molecular epidemiology and evolution of RNA viruses and the development of computational methods for understanding these.
Combining whole genome sequencing and network models to understand the epidemiology of bovine TB in the UK
Dr Roman Biek, University of Glasgow, UK
Abstract
Quantifying transmission dynamics of pathogens infecting multiple host species can pose significant research challenges, especially when the sampling process is biased towards certain types of host. This is exemplified by Mycobacterium bovis, the bacterium causing bovine TB (bTB) in cattle. In the UK, badgers are considered an important wildlife reservoir for bTB, which is thought to prevent the successful eradication of the disease from cattle. However, despite considerable research effort, the epidemiological role badgers play in maintaining and spreading bTB to cattle is still poorly understood. Here, we show how whole genome sequencing (WGS) technology can be combined with high-resolution data on contact networks of cattle to shed new light onto this problem. Focussing on a small cluster of infected cattle and badger samples from Northern Ireland, we provide the first direct genetic evidence of M bovis persistence on farms over multiple outbreaks with a continued, ongoing interaction with local badgers. In addition to providing novel insights into bTB epidemiology, even at extremely local scales, our study suggests that WGS based on more extensive sampling will allow quantification of the extent and direction of M bovis transmission between cattle and badgers, especially in situations where detailed demographic and contact data for cattle are also available.
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Dr Roman Biek, University of Glasgow, UK
Dr Roman Biek, University of Glasgow, UK
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Biography
Roman Biek currently holds a lectureship position at the University of Glasgow. His research aims to understand how infectious organisms spread and persist in animal populations, and how the ecological and evolutionary dynamics of pathogens are linked to those of their hosts and the physical environment. This research program is primarily pursued through the use of molecular markers and genetic inference, combined with field based investigations and epidemiological models. Apart from addressing basic questions in disease ecology and evolution, he is interested in providing solutions to applied problems in animal and human health. Such problems commonly arise since many of the pathogens he currently studies are shared between wildlife and domestic species or are transmissible to humans. While the majority of his work has been on RNA viruses (e.g. rabies, Ebola, oncogenic retroviruses in sheep, FIV, bluetongue), recent projects are also considering more slowly evolving pathogens (Mycobacterium bovis, Borrelia), facilitated by sequencing technologies that now permit studying molecular epidemiology based on full bacterial genomes.
Abstract
Quantifying transmission dynamics of pathogens infecting multiple host species can pose significant research challenges, especially when the sampling process is biased towards certain types of host. This is exemplified by Mycobacterium bovis, the bacterium causing bovine TB (bTB) in cattle. In the UK, badgers are considered an important wildlife reservoir for bTB, which is thought to prevent the successful eradication of the disease from cattle. However, despite considerable research effort, the epidemiological role badgers play in maintaining and spreading bTB to cattle is still poorly understood. Here, we show how whole genome sequencing (WGS) technology can be combined with high-resolution data on contact networks of cattle to shed new light onto this problem. Focussing on a small cluster of infected cattle and badger samples from Northern Ireland, we provide the first direct genetic evidence of M bovis persistence on farms over multiple outbreaks with a continued, ongoing interaction with local badgers. In addition to providing novel insights into bTB epidemiology, even at extremely local scales, our study suggests that WGS based on more extensive sampling will allow quantification of the extent and direction of M bovis transmission between cattle and badgers, especially in situations where detailed demographic and contact data for cattle are also available.
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Incorporating geographic information systems data into phylogenetic analysis
Dr Rebecca Gray, University of Oxford, UK
Abstract
Geographic information systems data (GIS) has been a valuable tool to correlate the spread of infectious diseases with environmental variables. Independently, molecular epidemiology relies upon pathogen genetic mutations that segregate in space and time, which are used in increasingly sophisticated evolutionary models to infer migration paths, rates, and population demography. Clearly a comprehensive approach that incorporates both GIS and evolutionary analyses would allow for rigorous hypothesis testing and greater understanding of the forces governing disease movements. I willdiscuss the advantages of using GIS in molecular epidemiological studies aswell as some of the current computational and theoretical challenges. I will present some recent work on West Nile Virus and rabies virus in which we have used information gained from the phylogeny on migration patterns within thecontext of GIS.
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Dr Rebecca Gray, University of Oxford, UK
Dr Rebecca Gray, University of Oxford, UK
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Rebecca received her PhD in Molecular Anthropology from the University of Florida in 2008 and completed a post-doctoral fellowship in the UF College of Medicine in 2011. She is currently an MRC Research Fellow in the Department of Zoology at the University of Oxford working with Oliver Pybus on molecular evolution of diseases.
As a molecular anthropologist, Rebecca’s broad interest focuses on the complexity of interactions between humans and infectious diseases. Her research spans multiple levels of analysis, including within-host evolution of HIV and Hep-C, to behavior of pathogens in global epidemics. She is interested in using tools of molecular evolution and GIS to uncover spatial patterns that can lead to greater understanding of pathogen behaviour.
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Antigenic flux in the influenza virus population
Dr Trevor Bedford, University of Edinburgh, UK
Abstract
Owing to rapid mutation, the evolution of the influenza virus occurs on a human timescale; rather than being forced to infer past evolutionary events, we can observe them in near real-time. While individuals develop long-lasting immunity to particular influenza strains after infection, antigenic mutations to the influenza virus genome result in proteins that are recognized to a lesser degree by the human immune system, leaving individuals susceptible to future infection. Mutations are only transiently advantageous; the virus population must keep evolving antigenically to stay ahead of developing human immunity. This talk focuses the process of antigenic innovation and the spread of novel strains through the human population. In this case, we have serological data from the hemagglutination inhibition (HI) assay comparing the level of cross-reactivity between different strains of influenza, as well as sequence data across strains. Here, we use a probabilistic framework called Bayesian multidimensional scaling (BMDS) to find a single consistent representation of antigenic distances between viruses by placing strains on a two-dimensional map. We integrate sequence evolution by treating BMDS location as a continuous diffusion across the phylogenetic tree. In this context, we examine the process of antigenic drift and investigate historical choices in vaccine strain by the World Health Organization.
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Dr Trevor Bedford, University of Edinburgh, UK
Dr Trevor Bedford, University of Edinburgh, UK
"Dr Trevor Bedford is a Newton International Fellow at the University of Edinburgh working in the field of evolutionary dynamics. Previously, Dr Bedford studied population genetics at Harvard University and disease dynamics at the University of Michigan. His work integrates population genetics, phylogenetics and epidemiological modeling to understand patterns of genetic and antigenic evolution in the human influenza virus. Additionally, he has studied the geographic circulation of virus populations. This work has a strong statistical and computational basis, using sequence data to arrive at an understanding of hidden underlying processes. Such an understanding of evolutionary and epidemiological processes contributes to successful surveillance and control strategies."
Multiscale evolutionary dynamics of HIV
Dr Katrina Lythgoe, Imperial College London, UK
Abstract
Through the use of next-generation sequencing, evidence is growing that ancestral HIV-1 genotypes (i.e. the viral genotypes observed during early infection) are, at least sometimes, preferentially transmitted over the majority virus circulating in a donor at the time of transmission. This ancestral virus probably persists at a low frequency within hosts due to the cycling of virus through very long-lived memory CD4+ T-Cells, a process that we call ‘store and retrieve’. We show how incorporating the store and retrieve process into our models can help explain two puzzling phenomena: (1) the fact that HIV-1 appears to evolve much faster within individuals than it does at the epidemic level and (2) the low levels of resistance found in developed countries despite the widespread use of antiretroviral drugs. The preferential transmission of ancestral virus needs to be properly integrated into evolutionary models if we are to accurately predict the evolution of immune escape, drug resistance and virulence in HIV-1 at the population level. Moreover, early infection viruses should be the major target for vaccine design, since these are the viral strains primarily involved in transmission.
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Dr Katrina Lythgoe, Imperial College London, UK
Dr Katrina Lythgoe, Imperial College London, UK
Dr Katrina Lythgoe is interested in applying ecological and evolutionary theory to better predict the evolutionary dynamics of infectious disease in humans and other species, with the ultimate aim of informing public health decisions. Her current research is focused on the within- and between-host evolution of HIV and in particular on the consequences of population structure on the evolutionary dynamics of the virus. She is a member of the Evolutionary Epidemiology Group within the Department of Infectious Disease Epidemiology, Imperial College London and currently holds a Wellcome Trust Re-Entry Fellowship. Before joining the group at Imperial, Dr Lythgoe was the Editor of Trends in Ecology of Evolution (TREE) for seven years.