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Emerging viruses: the phylodynamics of host jumps

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  • Full or part time
    Prof A Rambaut
    Prof M Woolhouse
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

Interested individuals should email their CV and statement of research interests to Professor Rambaut [Email Address Removed]

Supervisors: Prof. Andrew Rambaut and Prof. Mark Woolhouse (Institute of Evolutionary Biology, University of Edinburgh) and Dr Steve Baker (OUCRU, Vietnam)

Novel human viruses are reported every year. Most of these cause relatively localised disease problems but some, such as HIV or pandemic influenza, become major public health concerns. The processes through which a pathogen infects a new host species, adapts and subsequently ‘takes off’ are very poorly understood. Most novel viruses ultimately classified as pandemics have already had significant spread within human populations by the time they are detected (for example, 2009 H1N1 influenza pandemic [1], SARS or HIV). Conversely some animal viruses repeatedly jump to humans but never establish the sustained human to human transmission need to become a pandemic (some examples being H7N9 avian influenza in China in early 2013 [2] and more generally H5N1 avian influenza globally). A key question of concern is whether repeated host jumps allow viruses to successfully adapt to efficient human transmission or are viruses that form significant human epidemics those that by chance have the requisite characteristics for sustained transmission?

This study has 2 components. At the macroevolutionary scale, the student will collate and analyse public available sequence data on viruses and relate this to geographic range, transmission biology and and host range using state-of-the-art phylodynamics approaches implemented in the BEAST software package [3]. The evolutionary potential of certain pathogen lineages to jump hosts will be explored by mapping host species onto viral phylogenies using and extending models of discrete trait evolution available in BEAST [4]. At an epidemiological scale the student will have access to a rapidly growing collection of human and animal virus isolates obtained through the VIZIONS project based in Vietnam. This project is designed to deliver virus isolates collected in the field from both sides of the species barrier, with a focus on enteric viruses. These viruses are being sequenced by collaborators at the Sanger Institute and the student will analyse the resultant data set to quantify the rate of host switching and identify any recurrent genetic variants that precede or succeed host switching.

The successful applicant will have a mathematics or science degree, either a 1st or 2i, and possibly a MSc in statistics, bioinformatics or quantitative genetics. An interest in infectious diseases is helpful, though this project is about virus population dynamics rather than public health. Training will be provided in relevant statistical and analytical techniques and the successful applicant will work with researchers with a breadth of expertise in virus phylogenetics, epidemiology and evolution.


Smith et al. (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature. 459: 1122-1125.

Lam et al. (2013) The genesis and source of the H7N9 influenza viruses causing human infections in China. Nature. 502: 241–244.

Drummond et al. (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 29: 1969-1973.

Faria et al. (2013) Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints. Phil Trans Roy Soc B. 368: 1614-1619.

How good is research at University of Edinburgh in Biological Sciences?

FTE Category A staff submitted: 109.70

Research output data provided by the Research Excellence Framework (REF)

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