Who transmits infection to whom?

Katherine Atkins (primary)
Epidemiology of Population Health (Infectious Disease Epidemiology)
Julian Villabona-Arenas (secondary)
Epidemiology of Population Health (Infectious Disease Epidemiology)


Knowing the direction of transmission between two infected individuals provides a powerful insight into both the epidemiology and evolution of infectious disease. Recent methods have leveraged pathogen sequence data to identify the transmitting and recipient individual for multiple pathogens including viruses and bacteria. However, these methods vary in their accuracy across studies and across pathogens. To improve the accuracy of these methods we need to identify when they fail. Using a multidisciplinary approach, this project will work at the cutting edge of phylogenetics to improve current methods to identify the direction of transmission.


1. Christian Julian Villabona-Arenas, Stéphane Hué, James Baxter, Matthew Hall, Katrina A. Lythgoe, John Bradley, Katherine E. Atkins (2021) Using phylogenetics to accurately infer HIV-1 transmission direction. medRxiv https://doi.org/10.1101/2021.05.12.21256968

2. Chris Wymant, Matthew Hall, Oliver Ratmann, David Bonsall, Tanya Golubchik, Mariateresa de Cesare, Astrid Gall, Marion Cornelissen, Christophe Fraser, STOP-HCV Consortium, The Maela Pneumococcal Collaboration, and The BEEHIVE Collaboration (2018) PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity, Molecular Biology and Evolution 35(3):719–733 https://doi.org/10.1093/molbev/msx304

3. Matthew D Hall, Matthew TG Holden, Pramot Srisomang, Weera Mahavanakul, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Kay Fountain, Julian Parkhill, Emma K Nickerson, Sharon J Peacock, Christophe Fraser (2019) Improved characterisation of MRSA transmission using within-host bacterial sequence diversity eLife 2019;8:e46402 DOI: 10.7554/eLife.46402

Genes, development and STEM* approaches to biology
Area of Biology
Techniques & Approaches
BioinformaticsGeneticsMathematics / StatisticsSimulation / Modelling