Professor Oliver Pybus

Research Interests

Ancestry and diversification are processes unique to biology that shape every aspect of living systems, from individual cells to whole ecosystems. Using genome sequencing and other technologies we can now investigate these processes in unprecedented detail, and use the insights gained to tackle global challenges such as biodiversity loss, food production, and emerging epidemics. I feel fortunate to be a biologist at such an exciting time in the subject's history.

Most of my research concerns the evolutionary and ecological dynamics of infectious disease. Many pathogens evolve so rapidly that their ecology and evolution are coupled, requiring new inter-disciplinary methods of inquiry. Understanding this joint behaviour, sometimes called phylodynamics, is fundamental to applied problems including outbreak surveillance, vaccine design, and the evolution of drug resistance. I contribute to the theoretical development of phylodynamics and its application to public health and other fields. I develop new computational methods for the evolutionary analysis of genetic sequence data. More generally I am interested in topics at the interface of ecology and evolution, including molecular ecology, ancient DNA, portable genomics, spatial ecology, and statistical genetics.

Additional Information: I am a Professorial Fellow of New College and a Co-Director of the Oxford Martin School Programme on Pandemic Genomics. I am a Chief Editor of the open access journal Virus Evolution. I also hold a Professorship at the Royal Veterinary College.

For details of our current and past research please visit my research group website.

Selected Publications

Hoehn KB et al. (2019) Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. PNAS In press

Parag KV & Pybus OG (2019) Robust design for coalescent model inference. Systematic Biology 68:730-743

Faria NR et al. (2018) Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science 361:894–99

Thézé J et al. (2018) Genomic epidemiology reconstructs the introduction and spread of Zika virus in central America and Mexico. Cell Host & Microbe 23:855-64

Faria NR et al. (2017) Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546:406-10

Dudas G et al. (2017) Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 544:309-315

Grubaugh ND et al. (2017) Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature 546:401-05

Raghwani J et al. (2016) Exceptional heterogeneity in viral evolutionary dynamics characterises chronic hepatitis C virus infection. PLOS Pathogens 12:e1005894

Faria NR et al. (2016) Zika virus in the Americas: early epidemiological and genetic findings. Science 352:345–9

Hill SC et al. (2016) Antibody responses to avian influenza viruses in wild birds broaden with age. Proceedings of the Royal Society B 283:20162159

Lycett SJ et al. (2016) Role for migratory wild birds in the global spread of avian influenza H5N8. Science 354:213–7

Kobayashi Y et al. (2016) Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production. RNA Biology 13:883–94

Pybus OG, Tatem AJ, Lemey P (2015) Virus evolution and transmission in an ever-more connected world. Proceedings of the Royal Society B 282:20142878

Faria NR et al. (2014) The hidden history of HIV-1: establishment and early spread of the AIDS pandemic. Science 346:56-61

Lam TT et al. (2013) The genesis and source of the H7N9 influenza viruses causing human infections in China. Nature 502:241-4

Pybus OG et al. (2012) Unifying the spatial epidemiology and molecular evolution of emerging epidemics. PNAS 109:15066-71

List of site pages