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Fully funded 4-year PhD on modelling avian influenza outbreaks in the UK

Scholarship details:

  • A 4-year PhD studentship with a range of research training opportunities, including short courses in research, statistical, computational and generic skills
  • A tax-free stipend (£15,609/year in 2021/22)
  • £2,000/year research costs
  • Waiver of tuition fees for both UK and non-UK students

The 2022 Avian Influenza outbreak in the UK is largest on record and the first time farm-to-farm transmission and animal-to-human transmission has been identified[1]. Prior to 2022, the number of incidents increased year on year, with 310 incidents in 2020/2021. The increase in outdoor pig units and smallholder farms, together with changes in farming practices and wild bird migration routes and high population density contribute to the potential for a new influenza strain to emerge in the UK.

Avian Influenza is caused by Influenza A virus. Aquatic avian species are a natural reservoir; many other animals including swine, dogs and humans are susceptible to infection. Domesticated animals provide 'mixing’ hosts in which a reassortment between human and avian strains can give rise to a new pandemic – and this threat is poorly understood. Prior to 2020, a pandemic arising in this way was explicitly categorised as the greatest natural hazard likely to hit the UK in the next 5 years, and this has only been replaced by 'pandemics' to include other diseases in 2020.

Aims and objectives
The aim of this project is to address gaps in the scientific evidence base used to inform the control and management of Avian Influenza outbreaks in the UK.

  1. Characterise the temporal and spatial patterns of historical avian influenza outbreaks in the UK; Identify spatial hotspots for novel strain emergence using wild bird migrations, and domesticated poultry and pig populations;
  2. Develop an infectious disease model of avian influenza including cross-species transmission and spillover into the human population;
  3. Predict the potential impact of climate change on avian influenza outbreaks by affecting wild bird migration routes and timing.
    Objective 1: The student will use data on annual avian influenza outbreaks since 2005[3] to characterise seasonality and spatial patterns in wild birds, domesticated poultry and pigs. Patterns of outbreaks will be linked to anonymised Defra data on distribution of poultry and pig farms in the UK to identify spatial clustering with wild bird migration pathways and over-wintering sites. Spatial data on seasonal human influenza will be used to map potential sites and species where co-infection with avian and human strains might present a risk.

Objective 2: The student will develop a stochastic infectious disease model of spillover from birds to pigs to humans and the importance of cross-species transmission. We will use a similar framework to the model developed in [4], using data from [5] to constrain transmission routes within and between species.

Objective 3: The student will use publicly available data on annual, global wild bird migration routes together with local and global weather data to identify migration patterns which can be linked to year-to-year variation in weather, global cycles (like sudden stratospheric warmings/the El Niño–Southern Oscillation) and progressive climate change, with the aim of developing predictors of novel patterns of migration to inform risk analysis.

  1. Defra/APHA, Highly pathogenic avian influenza (HPAI) in the UK and Europe. Outbreak Assessment number 10. 2021.
  2. Jones et al. Global trends in emerging infectious diseases. Nature; 2008;451: 990–993.
  3. Alexander et al. Overview of Incursions of Asian H5N1 Subtype Highly Pathogenic Avian Influenza Virus into Great Britain, 2005–2008. AAVP 2010;54: 194–200.
  4. Brooks-Pollock, Wood. Eliminating bovine tuberculosis in cattle and badgers. Proc R Soc B Biol Sci. 2015;282.
  5. Nelson et al. Continual Reintroduction of Human Pandemic H1N1 Influenza A Viruses into Swine in the United States, 2009 to 2014. J Virol; 2015;89: 6218–6226.

For more details about the scholarships, see:

PhD position
University of Bristol
United Kingdom
Closing date
February 25th, 2022
Posted on
February 8th, 2022 14:38
Last updated
February 8th, 2022 14:38