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Influenza A virus evolution: Determining the key factors that influence emergence of influenza variants of animal and public health significance

  • Full or part time
  • Application Deadline
    Saturday, January 04, 2020
  • Funded PhD Project (UK Students Only)
    Funded PhD Project (UK Students Only)

Project Description

Our research aims to understand the complex evolutionary pathways that result in the emergence of influenza virus variants that pose a threat to human and animal health. The project will identify viral and host factors (particularly in poultry and pigs) which determine the potential for emergence into new hosts and explore how this understanding can be used to implement effective control measures such as vaccination.

We take an inter-disciplinary approach to One Health questions, by integrating surveillance, virology, ecology, and state-of-the-art antigenic and genetic computational analyses to understand pathogen evolution.

Along with training and guidance, you will have flexibility to shape the project according to your interests.

The candidate

You will ideally have a degree in the biological sciences and an interest in infectious diseases. Some previous experience with laboratory work or quantitative/computational methods is desirable but not required.

The institution

The PhD will utilize the resources and facilities at the OIE/FAO International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease at APHA-Weybridge as well as the Royal Veterinary College Hawkshead campus.

The supervisor

Dr Nicola Lewis is Associate Professor in Infectious Diseases and Co-ordinator of the Livestock Production and Health research programme at the RVC. Nicola is also Deputy Director of the OIE/FAO International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease at APHA-Weybridge. Her research focuses on investigating the ecology and evolution of influenza A viruses in multiple animal hosts and the risks that these viruses might pose to the human population, with a global context. This internationally collaborative high-impact research spans huge diversity from implementing surveillance in wild birds in the Republic of Georgia, analyzing emerging highly pathogenic avian influenza viruses, to using state-of-the-art computational techniques to analyse influenza virus antigenic and genetic evolution, to assess pandemic risk, and to inform international stakeholders on vaccine strains.


Applications must be complete, including both references, by 24th January 2020

Funding Notes

Fully funded place including home (UK) tuition fees and a tax-free stipend in the region of £17,009. Students from the EU are welcome to submit an application for funding, any offers will be subject to BBSRC approval and criteria.


Venkatesh, D; Poen, M J; Bestebroer, T M; Scheuer, R D; Vuong, O; Chkhaidze, M; Machablishvili, A; Mamuchadze, J; Ninua, L; Fedorova, N B; Halpin, R A; Lin, X; Ransier, A; Stockwell, T B; Wentworth, D E; Kriti, D; Dutta, J; Van Bakel, H; Puranik, A; Slomka, M J; Essen, S; Brown, I H; Fouchier, R A M; Lewis, N S.
Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem.

Poen, M.J. § , Venkatesh, D. § , Bestebroer, T.M., Vuong, O., Scheuer, R.D., Oude Munnink, B.B., de
Meulder, D., Richard, M., Kuiken, T., Koopmans, M.P.G., Kelder, L., Kim, Y.-J., Lee, Y.-J., Steensels, M., Lambrecht, B., Dan, A., Pohlmann, A., Beer, M., Savic, V., Brown, I.H., Fouchier, R.A.M., Lewis, N.S., 2019 . Co-circulation of genetically distinct highly pathogenic avian influenza A clade (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017–18.
Virus Evolution 5. § Equal contributions

Lewis, N S; Russell, C A; Langat, P; Anderson, T K; Berger, K; Bielejec, F; Burke, D F; Dudas, G; Fonville, J M; Fouchier, R A; Kellam, P; Koel, B F; Lemey, P; Nguyen, T; Nuansrichy, B; Peiris, J M; Saito, T; Simon, G; Skepner, E; Takemae, N; ESNIP3 Consortium; Webby R J; Van Reeth K; Brookes S M; Larsen L; Watson S J; Brown I H; Vincent A L.
The global antigenic diversity of swine influenza A viruses.
eLife, 5e12217. 2016

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