Predicting the Evolution of Influenza and SARS-CoV-2 Viruses

   Department of Zoology

  Prof D Smith, Prof H Baylis  Applications accepted all year round  Funded PhD Project (Students Worldwide)

About the Project

Our research focus is to design and develop analytical, computational, and mathematical methods to understand the fundamental processes that govern the evolution of influenza and SARS-CoV-2 viruses. In addition to the basic science core of the work, there is also the opportunity to translate this understanding into the prediction of future antigenic variants to guide phase II clinical trials of next generation influenza vaccines. Our research is highly interdisciplinary and involves substantial global collaboration with experimental virologists, immunologists and clinicians to quantify the selection pressures on influenza viruses in order to better understand their evolutionary dynamics, and to inform control strategies.

What the student will be doing:

The work in our group is theoretical and computational, in collaboration with experimental partners. Though this project is primarily computational, our group collaborates closely with experimental partners worldwide, e.g., Erasmus Medical Centre in the Netherlands and the University of Wisconsin in the United States.

Supervisor: Derek Smith

Derek Smith is Professor of Infectious Disease Informatics in the Zoology Department at Cambridge University. He is an advisor to the WHO influenza vaccine strain selection committee, and is also involved in vaccine strain selection for other human and non-human pathogens for the United Nations Food and Agriculture Organization and the World Animal Health Organisation. 

Derek’s research focuses on how pathogens evolve, to what extent this evolution is predictable, and determining public and animal health measures against such ever-changing pathogens. His group has developed vital computational tools for analysis and interpretation of antigenic variation and antibody responses to influenza and SARS-CoV-2. He has a long-standing interest in the effects of prior immunity and repeated vaccination. The combination of extensive knowledge of SARS-CoV-2 epidemiology and immunology with novel modelling and computational analyses has enabled him to answer fundamental questions about virus evolution and antibody mediated protection. During the COVID pandemic Derek contributed to SAGE, the UK Government Scientific Advisory Group for Emergencies and is a member of the US Government NIH SARS-CoV-2 Assessment of Viral Evolution (SAVE) Program.


If you are interested in this Project please email a copy of your CV together with a cover letter to

Biological Sciences (4)

Funding Notes

This project comes with a stipend which is highly competitive


Smith DJ, et al (2004) Mapping the Antigenic and Genetic Evolution of Influenza Virus. Science 305: 371-376.
Koel BF, et al (2013) Substitutions near the receptor binding site determine major antigenic change during influenza virus evolution. Science. Nov 22;342(6161):976-9. doi: 10.1126/science.1244730.
J. M. Fonville, S. H. Wilks, et al, (2014). Antibody landscapes after influenza virus infection or vaccination Science346(6212):996-1000. doi: 10.1126/science.1256427

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