Many micro-organisms, particularly RNA viruses, evolve so quickly that their evolutionary and epidemiological dynamics occur on a similar timescale and interact in complex ways. The nascent field of phylodynamics aims to understand and measure this relationship , by combining concepts from phylogenetics, epidemiology, population genetics and immunology.


Evolutionary and epidemiological processes can be combined by placing them on a common timescale or spatial frame of reference. This approach can be applied at hugely different biological scales, from studies of the global structure of pandemics to investigations of pathogen evolution within a single host.

Phylodynamics

  1. •Pybus OG, Rambaut A. 2009. Evolutionary analysis of the dynamics of viral infectious disease. Nature Reviews Genetics 10:540-50

  2. •Tee KK, Lam TT, Chan YF, Bible JM, Tong W, Kamarulzaman A, Takebe Y, Pybus OG. 2010. Evolutionary genetics of human enterovirus 71: Origin, population dynamics, natural selection and periodicity of the VP1 gene. Journal of Virology 84:3339-50

  3. •Pybus OG, Barnes E, Taggart R, Lemey P, Markov PV, Rasachak B, Syhavong B, Rattanaphone P, Sheridan I, Humphreys IS, Lu L, Newton P, Klenerman P. 2009. The genetic history of the hepatitis C virus in East Asia. Journal of Virology 83:1071-82

  4. •Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. 2008. The genomic and epidemiological dynamics of human influenza A virus. Nature 453:615-9

  5. •Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme A, Kellam P, and D. Pillay. 2007. Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of HIV-1. Journal of Virology 81:13050-6

  6. •de Oliveira T, Pybus OG, Rambaut A, Salemi M, Cassol S et al. 2006. Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature 444:836-7

  7. •Hué S, Pillay D, Clewley J, Pybus OG. 2005. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. PNAS 102:4425-9

  8. •Pybus OG, Drummond AJ, Nakano T, Robertson BH, Rambaut A. 2003. The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Molecular Biology & Evolution 20:381-7

  9. •Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC, Harvey PH. 2001. The epidemic behavior of the hepatitis C virus. Science 292:2323-5