Yuki Suzuki

(formerly Yuki Kobayashi)

Past group member

Current whereabouts: Assistant Professor,

Nihon University, Japan

My research concerns the evolutionary mechanisms of disease-causing RNA viruses. I am interested in the evolutionary factors that affect the antigenicity of influenza viruses, such as amino acid mutations, N-glycosylation, and the electronic charge of viral envelope proteins.  I also investigate compensatory amino acid evolution in influenza viruses.  I hope that revealing these mechanisms will help us to understand how influenza viruses escape from host immune responses. I am also studying the molecular epidemiology of rabies virus, especially strains that circulate among bats, and the evolution of endogenous borna-like nucleoproteins integrated into mammalian genomes.

Research Interests

Joe Parker

Gray RR, Parker J, Lemey P, Salemi M, Katzourakis A, Pybus OG. The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evolutionary Biology 11:131

Sahin GO, Bowles EJ, Parker J, Uchtenhagen H, Sheik-Khalil E, Taylor S, Pybus OG, Mäkitalo B, Walther-Jallow L, Spangberg M, Thorstensson R, Achour A, Fenyo EM, Stewart-Jones GB, Spetz AL. Generation of neutralizing antibodies and divergence of SIVmac239 in Cynomolgus macaques following short-term early antiretroviral therapy. PLOS Pathogens 6:e1001084

Tee KK, Pybus OG, Parker J, Ng KP, Kamarulzaman A, Takebe Y. Estimating the date of origin of an HIV-1 circulating recombinant form. Virology 387:229-34

Humphreys I, Fleming V, Fabris P, Parker J, Schulenberg B, Brown A, Demetriou C, Guadieri S, Pfafferott K, Lucas M, Collier J, Huang KH, Pybus OG, Klenerman P, Barnes E. Full length characterisation of the hepatitis C virus subtype 3a reveals novel hypervariable regions under positive selection during acute infection. Journal of Virology 83:11456-66

Parker J, Rambaut A, Pybus OG. Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infection, Genetics and Evolution 8:239-46

Past group member

Current whereabouts here






Selected Publications

Samir Bhatt

Past group member

Current whereabouts here




Bhatt S, Lam TT, Lycett SJ, Leigh Brown AJ, Bowden TA, Holmes EC, Wood JLN, Brown IH, Kellam P, COSI consortium, Pybus OG.The evolutionary dynamics of influenza A virus adaptation to mammalian hosts. Philosophical Transactions of the Royal Society Series B 368:20120382

Lycett SJ, Baillie G, Coulter E, Bhatt S, Kellam P, McCauley JW, Brown IH, Pybus OG, Wood JLN,  Leigh Brown AJ, COSI consortium. Estimating reassortment rates in co-circulating Eurasian swine influenza strains. Journal of General Virology 93:2326-36

Vijaykrishna D, Smith GJD, Pybus OG, Zhu H, Bhatt S, Poon LLM, Riley S, Bahl J, Ma SK, Cheung CL, Perera RAP, Chen H, Shortridge KF, Webby RJ, Webster RG, Guan Y, Peiris JSM. Long-term evolution and transmission dynamics of swine influenza A virus. Nature 473:519-22

Bhatt S, Holmes EC, Pybus OG. The genomic rate of molecular adaptation of the human influenza A virus. Molecular Biology & Evolution 28:2443-51

Bhatt S, Katzourakis A, Pybus OG. Detecting natural selection in RNA virus populations using sequence summary statistics. Infection Genetics & Evolution 10:421-30

Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CM, Raghwani J, Bhatt S, Peiris JS, Guan Y, Rambaut A. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122-5

Selected Publications

Robert Belshaw

Past group member

Current whereabouts here

Rebecca Rose

(formerly Rebecca Gray)

Rose R, Markov PV, Lam TT, Pybus OG. Viral evolution explains the associations among hepatitis C virus genotype, clinical outcomes, and human genetic variation. Infection, Genetics & Evolution 20:418-21

Gray RR, Tanaka Y, Takebe Y, Magiorkinis G, Buskell Z, Seeff L, Alter H, Pybus OG. Evolutionary analysis of hepatitis C virus gene sequences from 1953. Philosophical Transactions of the Royal Society Series B 368:20130168

Pybus OG, Gray RR. The virus whose family expanded. Nature 498:310-11

Gray RR, Salemi M, Klenerman P, Pybus OG. A new evolutionary model for hepatitis C virus chronic infection. PLOS Pathogens 8:e1002656

Gray RR, Strickland S, Veras NM, Goodenow MM, Pybus OG, Lemon S, Fried M, Nelson DR, Salemi M.  Unexpected maintenance of hepatitis C virus diversity following liver transplantation. Journal of Virology 86:8432-9

Pybus OG, Suchard M, Lemey P, Bernardin F, Rambaut A, Crawford FW, Gray RR, Arinaminpathy N, Stramer S, Busch MP, Delwart E. Unifying the spatial epidemiology and molecular evolution of emerging epidemics. Proceedings of the National Academy of Sciences USA 109:15066-71

RR Gray*, J Parker*, P Lemey, M Salemi, A Katzourakis, OG Pybus. The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evolutionary Biology 11:131

RR Gray, OG Pybus, M Salemi. Measuring the temporal structure in serially-sampled phylogenies. Methods in Ecology & Evolution 2:437-45

RR Gray, AJ Tatem, JA Johnson, AV Alekseyenko, OG Pybus, MA Suchard, M Salemi. Bayesian phylogenetics of bacterial genomes: inferring the pandemic spread of Methicillin resistant Staphylococcus aureus ST239. Molecular Biology & Evolution 28: 1593-1603

Past group member

Selected Publications

Aris Katzourakis

Past  group member

More information can be found at Aris’ new website




James Iles

Past group member

Current whereabouts here





Iles JC, Njouom R, Foupouapouognigni Y, Bonsall D, Bowden R, Trebes A, Piazza P, Barnes E, Pépin J, Klenerman P, Pybus OG (2015) Characterisation of hepatitis C virus recombination in Cameroon by use of nonspecific next-generation sequencing. Journal of Clinical Microbiology 53:3155–64

Iles JC, Raghwani J, Harrison GLA, Pepin J, Djoko CF, Tamoufe U, Lebreton M, Schneider BS, Fair JN, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Wolfe ND, Simmonds P, Klenerman P, Pybus OG (2014) Phylogeography and molecular epidemiology of hepatitis C virus genotype 4 in Africa. Virology 464-465:233-43

Markov PV, Gray RR, Iles JC, Pybus OG. The evolutionary epidemiology of the hepatitis C virus. In Parasite diversity and diversification: evolutionary ecology meets phylogenetics (S. Morand, B. Krasnov, T. Littlewood, eds.) Cambridge University Press. In press

Iles JC, Harrison GLA, Lyons S, Djoko CF, Tamoufe U, Lebreton M, Schneider BS, Fair JN, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Wolfe ND, Klenerman P, Simmonds P, Pybus OG (2013) Hepatitis C virus infections in the Democratic Republic of Congo exhibit a cohort effect. Infection, Genetics & Evolution 19:386-94

Selected Publications

Simon Dellicour

Past group member

Current whereabouts here

My current work focuses on the development of an analytical framework that can compare viral genetic information and ecological landscape data in order to statistically test for significant associations between viral movement and underlying ecological variables (e.g. population density, elevation, etc). The specific aims of my project are (i) to incorporate uncertainty related to phylogenetic inference, (ii) to allow the analysis of time-series environmental data (e.g. temperature) and (iii) to evaluate the whole method using null models and empirical data.

Research Interests

Patrick Hoscheit

Past group member

Current whereabouts here

I am a researcher in the MaIAGE unit of the French Agronomical Research Institute (INRA), visiting the team for a year. My research deals with applying mathematical tools (especially random trees and graphs) to problems in epidemiology. Here in Oxford, I am mainly concerned with developing new models for viral populations under strong positive selection. Other areas of interest include (i) random tree theory, particularly continuum trees, (ii) branching processes and their applications in biology, (iii) population genetics, especially relating to experimental evolution and (iv) epidemics on random graph models.

Research Interests

Jing Lu

Past group member

Current whereabouts: Guangdong CDC, China

My research centers on the evolutionary and epidemiological investigation of emerging viruses and on virus-host interactions. My current research involves the genetic evolution of novel H7N9 avian influenza viruses and enteroviruses that cause hand foot and mouth diseases. I am also working on other human viruses including norovirus, poliovirus and measles virus.

Research Interests