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Centre for Pathogen Evolution


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

Supervisor - Prof Derek Smith 

Applications accepted all year round, please contact .

Project summary: 

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.


The successful candidate should have an Honours Degree at 2.1 or above (or equivalent). Candidates whose first language is not English should have an IELTS score of 7.0 or equivalent

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 influenza antigenic variation and antibody responses to influenza. He has a long-standing interest in the effects of prior immunity and repeated vaccination. The combination of extensive knowledge of influenza epidemiology and immunology with novel modelling and computational analyses has enabled him to answer fundamental questions about virus evolution and antibody mediated protection.

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Key Publications

Derek J. Smith, Alan S. Lapedes, et al, (2004). Mapping the Antigenic and Genetic Evolution of Influenza Virus Science 305(5682):371-376.

Colin A. Russell, Terry C. Jones, et al, (2008). The Global Circulation of Seasonal Influenza A (H3N2) Viruses Science 320(5874):340-346.

Björn F. Koel, David F. Burke, et al, (2013). Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution Science 342(6161):976-979.

J. M. Fonville, S. H. Wilks, et al, (2014). Antibody landscapes after influenza virus infection or vaccination Science 346(6212):996-1000

Samuel H. Wilks, Barbara Mühlemann et al, (2022) Mapping SARS-CoV-2 antigenic relationships and serological responses bioRxiv