Institute for Emerging Infections


Dr. Aris Katzourakis


Phone: +44 (0) 1865 281223


I studied biology at Imperial College, London, followed by a PhD in evolutionary biology at Imperial College (Silwood Park campus).  After a brief visiting fellowship at the European Bioinformatics Institute (Hinxton, Cambridge), I joined the Evolutionary Biology group at Oxford, on an MRC fellowship, in 2004.  In 2007 I joined the Epidemiology and Infectious Disease group also at Oxford.

Research Activities

My research interests include viral evolution, genome evolution, and mobile genetic element evolution. I am particularly interested in retroviruses, such as the endogenous retroviruses that constitute a substantial fraction of vertebrate genomes, and exogenous retroviruses such as HIV. My research primarily involves using gene sequence data to address evolutionary questions such as why certain retroviruses are more likely to cross species boundaries than others, what host factors affect retroviral activity, when and where did different viral groups originate? I am also interested in methods of evolutionary inference from gene sequence data.

Other information

I am a JRF at New College.  I also currently serve on the editorial board of Evolutionary Biology.


Katzourakis, A., Gifford, R. J., Tristem, M., Gilbert, M. T. P., Pybus, O. G. (2009).  Macroevolution of complex retroviruses. Science 325: 1512.

Bhatt, S., Katzourakis, A., Pybus, O. G. (2009). Detecting natural selection in RNA virus populations using sequence summary statistics. Infection, Genetics & Evolution. (in press).

Huang K-H, Goedhals, D, Fryer, H, van Vuuren, C., Katzourakis, A., De Oliveira, T., Cassol, S., Seebregts, C., McLean, A. R., Klenerman, P., Phillips, R. E., Frater, J. (2009).  Low CD4 cell counts are associated with pre-therapy HIV drug resistance. Antiviral Therapy. (in press).

Matthews, P. C., Leslie, A. J., Katzourakis, A., Crawford, H., Payne, R., Prendergast, A., Power, K., Kelleher, A. D., Klenerman, P., Carlson, J., Heckerman, D., Nudng’u, T., Walker, B. D., Allen, T. M., Pybus, O. G., Goulder, P. J. (2009).  HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering.  Journal of Virology 83: 4605-4615.

Switzer, W. M., Salemi, M. Qari, S. H., Jia, H., Gray, R. R., Katzourakis, A., Marriott, S. J., Pryor, K. N., Wolfe, N. D., Burke, D. S., Folks, T. M., Heneine, W.  (2009).  Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4. Retrovirology 6:9.

Keckesova, Z., Ylinen, L. M. J., Towers, G. J., Gifford, R. J., Katzourakis, A.  (2009).  Identification of a RELIK orthologue in the genome of the European hare (Lepus Europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology 384: 7-11.

Gifford R. J. *, Katzourakis, A.*, Tristem, M., Pybus, O. G., Winters, M., Shafer, R. W. (2008).  A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution.  Proceedings of the National Academy of Sciences USA 105: 20362-20367.
(* Equal contributions).

Armitage, A. E., Katzourakis, A., de Oliveira T., Welch, J. J., Belshaw, R., Bishop, K. N., Kramer, B., McMichael, A. J., Malim, M. H., Rambaut, A., Iversen, A. K. N. (2008).  Conserved footprints of APOBEC3G on hypermutated HIV-1 and HERV-K(HML2) sequences.  Journal of Virology 82: 8743-8761.  

Katzourakis, A., Pereira, V., Tristem, M. (2007).  Effects of recombination rate on human endogenous retrovirus fixation and persistence.  Journal of Virology 81: 10712-10717.  (Selected by Faculty of 1000).

Belshaw, R., Watson, J., Katzourakis, A., Howe, A., Woolven-Allen, J., Burt, A., Tristem, M. (2007).  Rate of recombinational deletion among human endogenous retroviruses.  Journal of Virology 81: 9437-9442.

Katzourakis, A., Tristem, M., Pybus, O.G., Gifford, R. J. (2007).  Discovery and analysis of the first endogenous lentivirus.  Proceedings of the National Academy of Sciences USA 104: 6261-6265.  (See also associated commentary in PNAS, Science News Magazine, and Selected by Faculty of 1000).

Katzourakis, A., Rambaut, A., Pybus, O.G. (2005).  The evolutionary dynamics of endogenous retroviruses.  Trends in Microbiology 13: 463-468.

Belshaw, R., Katzourakis, A., Paces, J., Burt, A., Tristem, M.  (2005).  High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to re-infection.  Molecular Biology and Evolution 22: 814-817.

Belshaw, R., Katzourakis, A. (2005).  BlastAlign: a program that uses blast to align problematic nucleotide sequences.  Bioinformatics 21 (1): 122-123.

Katzourakis, A., Tristem, M. (2005).  Phylogeny of human endogenous and exogenous retroviruses.  In: Retroviruses and primate genome evolution (E. D. Sverdlov, ed.). 186-203.

Belshaw, R., Pereira, V., Katzourakis, A., Talbot, G., Paces, J., Burt, A., Tristem, M.  (2004).  Long-term reinfection of the human genome by endogenous retroviruses.  Proceedings of the National Academy of Sciences USA 101: 4894-4899.

Purvis, A., Katzourakis, A., Agapow, P. M. (2002).  Evaluating phylogenetic tree shape: Two modifications to Fusco & Cronk's method.  Journal of Theoretical Biology 214 (1): 99-103.

Katzourakis, A., Purvis, A. Azmeh, S., Rotheray, G., Gilbert, F. (2001).  Macroevolution of hoverflies (Diptera: Syrphidae): the effect of using higher taxa in studies of biodiversity, and correlates of species richness.  Journal of Evolutionary Biology 14: 219-227.