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Interdisciplinary Perspectives on Infectious Diseases
Volume 2011 (2011), Article ID 238743, 9 pages
Contact Heterogeneity and Phylodynamics: How Contact Networks Shape Parasite Evolutionary Trees
1Section of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
2Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
3Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
Received 4 June 2010; Accepted 15 October 2010
Academic Editor: Katia Koelle
Copyright © 2011 Eamon B. O'Dea and Claus O. Wilke. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- B. T. Grenfell, O. G. Pybus, J. R. Gog et al., “Unifying the epidemiological and evolutionary dynamics of pathogens,” Science, vol. 303, no. 5656, pp. 327–332, 2004.
- E. C. Holmes and B. T. Grenfell, “Discovering the phylodynamics of RNA viruses,” PLoS Computational Biology, vol. 5, no. 10, Article ID e1000505, 2009.
- J. J. Siebenga, P. Lemey, S. L. Kosakovsky Pond, A. Rambaut, H. Vennema, and M. Koopmans, “Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants,” PLoS Pathogens, vol. 6, no. 5, Article ID e1000884, 2010.
- C. Fraser, C. A. Donnelly, S. Cauchemez et al., “Pandemic potential of a strain of influenza A (H1N1): early findings,” Science, vol. 324, no. 5934, pp. 1557–1561, 2009.
- G. J. D. Smith, D. Vijaykrishna, J. Bahl et al., “Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic,” Nature, vol. 459, no. 7250, pp. 1122–1125, 2009.
- A. Rambaut and E. C. Holmes, “The early molecular epidemiology of the swine-origin A/H1N1 human inuenza pandemic,” PLoS Currents: Influenza, vol. 1, article RRN1003, 2009.
- G. J. Hughes, E. Fearnhill, D. Dunn, S. J. Lycett, A. Rambaut, and A. J. Leigh Brown, “Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom,” PLoS Pathogens, vol. 5, no. 9, Article ID e1000590, 2009.
- R. Biek, J. C. Henderson, L. A. Waller, C. E. Rupprecht, and L. A. Real, “A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 19, pp. 7993–7998, 2007.
- T. Nakano, L. Lu, Y. He, Y. Fu, B. H. Robertson, and O. G. Pybus, “Population genetic history of hepatitis C virus 1b infection in China,” Journal of General Virology, vol. 87, no. 1, pp. 73–82, 2006.
- S. N. Bennett, A. J. Drummond, D. D. Kapan et al., “Epidemic dynamics revealed in dengue evolution,” Molecular biology and evolution, vol. 27, no. 4, pp. 811–818, 2010.
- E. M. Volz, S. L. Kosakovsky Pond, M. J. Ward, A. J. Leigh Brown, and S. D.W. Frost, “Phylodynamics of infectious disease epidemics,” Genetics, vol. 183, no. 4, pp. 1421–1430, 2009.
- A. J. Drummond and A. Rambaut, “BEAST: Bayesian evolutionary analysis by sampling trees,” BMC Evolutionary Biology, vol. 7, no. 1, article 214, 2007.
- V. N. Minin, E. W. Bloomquist, and M. A. Suchard, “Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics,” Molecular Biology and Evolution, vol. 25, no. 7, pp. 1459–1471, 2008.
- S. Bansal, B. T. Grenfell, and L. A. Meyers, “When individual behaviour matters: homogeneous and network models in epidemiology,” Journal of the Royal Society Interface, vol. 4, no. 16, pp. 879–891, 2007.
- F. Liljeros, C. R. Edling, and L. A. N. Amaral, “Sexual networks: implications for the transmission of sexually transmitted infections,” Microbes and Infection, vol. 5, no. 2, pp. 189–196, 2003.
- P. Erdős and A. Renyi, “On random graphs. I,” Publicationes Mathematicae, vol. 6, pp. 290–297, 1959.
- F. Viger and M. Latapy, “Efficient and simple generation of random simple connected graphs with prescribed degree sequence,” in Computing and Combinatorics, pp. 440–449, Springer, Berlin, Germany, 2005.
- D. T. Gillepsie, “A general method for numerically simulating the stochastic time evolution of coupled chemical reactions,” Journal of Computational Physics, vol. 22, no. 4, pp. 403–434, 1976.
- D. T. Gillespie, “Stochastic simulation of chemical kinetics,” Annual Review of Physical Chemistry, vol. 58, pp. 35–55, 2007.
- M. Galassi, J. Davies, J. Theiler, et al., GNU Scientific Library Reference Manual, Network Theory Ltd., 3rd edition, 2009.
- G. Csardi and T. Nepusz, “The igraph software package for complex network research,” InterJournal, vol. Complex Systems, p. 1695, 2006.
- A. Rambaut and A. J. Drummond, “Tracer v1.5,” 2009, http://beast.bio.ed.ac.uk/Tracer.
- J. F. C. Kingman, “On the genealogy of large populations,” Journal of Applied Probability, vol. 19, pp. 27–43, 1982.
- S. D.W. Frost and E. M. Volz, “Viral phylodynamics and the search for an effective number of infections,” Philosophical Transactions of the Royal Society B, vol. 365, no. 1548, pp. 1879–1890, 2010.
- J. Wakeley and O. Sargsyan, “Extensions of the coalescent effective population size,” Genetics, vol. 181, no. 1, pp. 341–345, 2009.
- M. Barthélemy, A. Barrat, R. Pastor-Satorras, and A. Vespignani, “Velocity and hierarchical spread of epidemic outbreaks in scale-free networks,” Physical Review Letters, vol. 92, no. 17, Article ID 178701, 2004.
- M. Barthélemy, A. Barrat, R. Pastor-Satorras, and A. Vespignani, “Dynamical patterns of epidemic outbreaks in complex heterogeneous networks,” Journal of Theoretical Biology, vol. 235, no. 2, pp. 275–288, 2005.
- E. Volz, “SIR dynamics in random networks with heterogeneous connectivity,” Journal of Mathematical Biology, vol. 56, no. 3, pp. 293–310, 2008.
- J. C. Miller, “Spread of infectious disease through clustered populations,” Journal of the Royal Society Interface, vol. 6, no. 41, pp. 1121–1134, 2009.
- E. Volz and L. A. Meyers, “Susceptible-infected-recovered epidemics in dynamic contact networks,” Proceedings of the Royal Society B, vol. 274, no. 1628, pp. 2925–2933, 2007.
- M. Altmann, “Susceptible-infected-removed epidemic models with dynamic partnerships,” Journal of Mathematical Biology, vol. 33, no. 6, pp. 661–675, 1995.
- M. Morris and M. Kretzschmar, “A microsimulation study of the effect of concurrent partnerships on the spread of HIV in Uganda,” Mathematical Population Studies, vol. 8, pp. 109–133, 2000.
- E. Volz and L. A. Meyers, “Epidemic thresholds in dynamic contact networks,” Journal of the Royal Society Interface, vol. 6, no. 32, pp. 233–241, 2009.
- B. D. O'Fallon, J. Seger, and F. R. Adler, “A continuous-state coalescent and the impact of weak selection on the structure of gene genealogies,” Molecular Biology and Evolution, vol. 27, no. 5, pp. 1162–1172, 2010.
- D. Welch, G. K. Nicholls, A. Rodrigo, and W. Solomon, “Integrating genealogy and epidemiology: the ancestral infection and selection graph as a model for reconstructing host virus histories,” Theoretical Population Biology, vol. 68, no. 1, pp. 65–75, 2005.
- A. J. Drummond, A. Rambaut, B. Shapiro, and O. G. Pybus, “Bayesian coalescent inference of past population dynamics from molecular sequences,” Molecular Biology and Evolution, vol. 22, no. 5, pp. 1185–1192, 2005.
- Z. Yang, Computational Molecular Evolution, Oxford Series in Ecology and Evolution, Oxford University Press, Oxford, Miss, USA, 2006.
- J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2nd edition, 2003.
- P. Lemey, M. Salemi, and A.-M. Vandamme, Eds., The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Cambridge University Press, Cambridge, Mass, USA, 2nd edition, 2009.
- G. I. Hagstrom, D. H. Hang, C. Ofria, and E. Torng, “Using Avida to test the effects of natural selection on phylogenetic reconstruction methods,” Artificial Life, vol. 10, no. 2, pp. 157–166, 2004.
- T. Stokes and P. Schober, “A survey of contact tracing practice for sexually transmitted diseases in GUM clinics in England and Wales,” International Journal of STD and AIDS, vol. 10, no. 1, pp. 17–21, 1999.
- M. McCarthy, L. J. Haddow, V. Furner, and A. Mindel, “Contact tracing for sexually transmitted infections in New South Wales, Australia,” Sexual Health, vol. 4, no. 1, pp. 21–25, 2007.
- J. S. St. Lawrence, D. E. Montaño, D. Kasprzyk, W. R. Phillips, K. Armstrong, and J. S. Leichliter, “STD screening, testing, case reporting, and clinical and partner notification practices: a national survey of US physicians,” American Journal of Public Health, vol. 92, no. 11, pp. 1784–1788, 2002.
- R. K. W. Chan, H. H. Tan, M. T. W. Chio, P. Sen, K. W. Ho, and M. L. Wong, “Sexually transmissible infection management practices among primary care physicians in Singapore,” Sexual Health, vol. 5, no. 3, pp. 265–271, 2008.
- C. Heal and R. Muller, “General practitioners' knowledge and attitudes to contact tracing for genital Chlamydia trachomatis infection in North Queensland,” Australian and New Zealand Journal of Public Health, vol. 32, no. 4, pp. 364–366, 2008.
- Y. Ruan, C. L. Wei, L. A. Ee et al., “Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection,” Lancet, vol. 361, no. 9371, pp. 1779–1785, 2003.
- C. A. Donnelly, A. C. Ghani, G. M. Leung et al., “Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong,” Lancet, vol. 361, no. 9371, pp. 1761–1766, 2003.
- F. Fenner, D. A. Henderson, I. Arita, Z. Jezek, and I. D. Ladnyi, Smallpox and Its Eradication, vol. 6 of History of International Public Health, World Health Organization, Geneva, Switzerland, 1988.
- R. B. Rothenberg, P. D. McElroy, M. A. Wilce, and S. Q. Muth, “Contact tracing: comparing the approaches for sexually transmitted diseases and tuberculosis,” International Journal of Tuberculosis and Lung Disease, vol. 7, no. 12, pp. S342–S348, 2003.
- J. C. Stack, J. D. Welch, M. J. Ferrari, B. U. Shapiro, and B. T. Grenfell, “Protocols for sampling viral sequences to study epidemic dynamics,” Journal of the Royal Society Interface, vol. 7, no. 48, pp. 1119–1127, 2010.
- C. T. T. Edwards, E. C. Holmes, D. J. Wilson et al., “Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1,” BMC Evolutionary Biology, vol. 6, article no. 28, 2006.
- J. J. Potterat, L. Phillips-Plummer, S. Q. Muth et al., “Risk network structure in the early epidemic phase of HIV transmission in Colorado Springs,” Sexually Transmitted Infections, vol. 78, no. 1, pp. i159–i163, 2002.
- R. B. Rothenberg, D. M. Long, C. E. Sterk et al., “The Atlanta urban networks study: a blueprint for endemic transmission,” AIDS, vol. 14, no. 14, pp. 2191–2200, 2000.
- J. Wallinga, P. Teunis, and M. Kretzschmar, “Using data on social contacts to estimate age-specific transmission parameters for respiratory-spread infectious agents,” American Journal of Epidemiology, vol. 164, no. 10, pp. 936–944, 2006.
- N. Hens, N. Goeyvaerts, M. Aerts, Z. Shkedy, P. Van Damme, and P. Beutels, “Mining social mixing patterns for infectious disease models based on a two-day population survey in Belgium,” BMC Infectious Diseases, vol. 9, article no. 5, 2009.
- J. Mossong, N. Hens, M. Jit et al., “Social contacts and mixing patterns relevant to the spread of infectious diseases,” PLoS Medicine, vol. 5, no. 3, article no. e74, 2008.
- M. E. Craft, E. Volz, C. Packer, and L. A. Meyers, “Distinguishing epidemic waves from disease spillover in a wildlife population,” Proceedings of the Royal Society B, vol. 276, no. 1663, pp. 1777–1785, 2009.
- D. J. Salkeld, M. Salathé, P. Stapp, and J. H. Jones, “Plague outbreaks in prairie dog populations explained by percolation thresholds of alternate host abundance,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 32, pp. 14247–14250, 2010.
- L. A. Meyers, B. Pourbohloul, M. E. J. Newman, D. M. Skowronski, and R. C. Brunham, “Network theory and SARS: predicting outbreak diversity,” Journal of Theoretical Biology, vol. 232, no. 1, pp. 71–81, 2005.
- S. Eubank, “Network based models of infectious disease spread,” Japanese Journal of Infectious Diseases, vol. 58, no. 6, pp. S9–S13, 2005.
- L. M. Sander, C. P. Warren, I. M. Sokolov, C. Simon, and J. Koopman, “Percolation on heterogeneous networks as a model for epidemics,” Mathematical Biosciences, vol. 180, pp. 293–305, 2002.