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Conservation Research Institute



Department of Veterinary Medicine

Use of mathematical and statistical modelling to understanding the dynamics and evolution of infectious diseases such as HIV, hepatitis C and influenza A.

Simon Frost is accepting applications for PhD students.

Simon Frost is available for consultancy.


My research interests focus on the use of mathematical and statistical modeling to understanding the dynamics and evolution of infectious diseases such as HIV, hepatitis C and influenza A. My work covers both within- and between-host dynamics, and while my past research has focused on viruses, it is broadening to examine the role of contact structure and heterogeneity in the host population.

Current projects include:

  • The dynamics and evolution of viruses, especially emerging infections
  • Analysis of viromes, to identify uncharacterised viruses, in samples from humans as well as non-humans
  • B cell repertoire dynamics, particularly in the context of immunisation and infection
Our work covers a wide range of virus-host systems, including HIV and simian retroviruses, enteric viruses such as norovirus and rotavirus, hepatitis viruses, including HBV, HCV, and HEV, as well as viruses that have yet to be associated with pathological consequences such as pegiviruses and anelloviruses.


Key publications: 

Frost, S.D.W. and Volz, E.M. 2013. Modeling tree shape and structure in viral phylodynamics. Phil. Trans. Roy. Soc. B., in press.

Volz, E., Koopman, J.S., Ward, M.J., Leigh Brown, A.J., and Frost, S.D.W. 2012. Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comp. Biol.

McCreesh, N., Frost, S.D.W., Seeley, J., Katongole, J., Ndagire Tarsh, M., Ndungutse, R., Jichi, F., Tilson, M., Maher, D., Johnston, L.G., Sonnenberg, P., Copas, A., Hayes, R.J., and White, R.G. (2012) Empirical evaluation of Respondent-Driven Sampling. Epidemiology 23:138-147.

Drumright, L.N. and Frost, S.D.W. 2010 Rapid social network assessment for predicting HIV and STI risk among men attending bars and clubs in San Diego, California. Sex. Transm. Infect. 86 Suppl 3:iii17-23.

Frost, S.D.W. and Volz, E.M. 2010 Viral phylodynamics and the search for an `effective number of infections'. Phil. Trans. Roy. Soc. B. 365:1879-1890.

Volz, E.M., Kosakovsky Pond, S.L., Ward, M.J., Leigh Brown, A. J., and Frost, S.D.W. 2009 Phylodynamics of infectious disease dynamics. Genetics 183:1421-1430.

Poon, A.F.Y., Brouwer, K.C., Strathdee, S.A., Firestone-Cruz, M., Lozada, R.M., Pond, S.L., Heckathorn, D.D., and Frost, S.D.W. (2009) Parsing social network survey data from hidden populations using stochastic context-free grammars. PLoS One 4:e6777.

Frost, S.D.W. 2007 Using sexual affiliation networks to describe the sexual structure of a population. Sex. Transm. Inf. 83: (suppl 1): 137-142

Poon, A.F.Y., Kosakovsky Pond, S.L., Bennett, P., Richman, D.D., Leigh Brown, A.J. and Frost, S.D.W. 2007 Adaptation to human populations is revealed by within-host polymorphism in HIV-1 and Hepatitis C virus. PLoS Pathog. 3:e45

Poon, A.F.Y., Lewis, F.I., Kosakovsky Pond, S.L. and Frost, S.D.W. 2007 Detection of 'N-linked' glycan interactions by phylogenetic and Bayesian network analysis og HIV-1 envelope sequesces. PLoS Comp. Biol. 3:e45

Frost, S.D.W. Brouwer, K.C., Firestone, M.A., Ramos, R., Ramos, M.E., Lozada, R.M., Magis-Rodriquez, C. and Strathdee, S.A. 2006 Respondent driven sampling of injection drug users in two U.S.- Mexico border cities: recruitment dynamics and impact on estimates of HIV and syphilis prevalence. J. Urban Health. 83: (suppl 7): 83-97

Kosakovsky Pond, S.L., Posada, D., Gravenor, M.B., Woelk, C.H. and Frost, S.D.W.2006 Automated phylogenetic detection of recombination using a genetic algorithm. Mol.Biol.Evol. 23: 1891-1901

Frost, S.D.W., Wrin, T., Smith, D.M., Kosakovsky Pond, S.L., Liu, Y., Paxinos, E., Chappey, C., Galovich, J., Beauchaine, J., Petropoulos, C.J., Little, S.J. and Richman, D.D. 2005 Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc.Natl.Acad.Sci. 102: 18514-18519

Frost, S.D.W., Liu, Y., Kosakovksy Pond, S.L., Chappey, C., Liu, Y., Wrin, T., Petropoulos, C.J., Little, S.J. and Richman, D.D. 2005 Characterization of HIV-1 envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. Journal of Virology 79: 6523-6527

Kosakovsky Pond, S.L. and Frost, S.D.W., 2005 Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22: 1208-1222

Frost, S.D.W., Martinez-Picado, J., Ruiz, L., Clotet, B., and Leigh Brown, A.J. 2002 Viral dynamics during structured therapy interruptions of chronic human immunodeficiency virus type 1 infection. J. Virol. 76:968-979.

Frost, S.D.W., Dumaurier, M.-J., Wain-Hobson, S. and Leigh Brown, A.J. 2001 Genetic drift and within-host metapopulation dynamics of HIV-1 infection. Proc. Natl. Acad. Sci. USA 98:6975-6980.

Reader in Pathogen Dynamics


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