2009
DOI: 10.1534/genetics.109.106021
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Phylodynamics of Infectious Disease Epidemics

Abstract: We present a formalism for unifying the inference of population size from genetic sequences and mathematical models of infectious disease in populations. Virus phylogenies have been used in many recent studies to infer properties of epidemics. These approaches rely on coalescent models that may not be appropriate for infectious diseases. We account for phylogenetic patterns of viruses in susceptibleinfected (SI), susceptible-infected-susceptible (SIS), and susceptible-infected-recovered (SIR) models of infecti… Show more

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Cited by 222 publications
(333 citation statements)
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“…However, for both the Swedish and Finnish data sets, the epidemic dynamics shown by the above ML analyses were also captured by Bayesian analyses, using a relaxed clock and two different growth models (the nonparametric skyline growth model and the logistic growth model). This allowed us to infer when epidemic events occurred ( This coincides with the increase in newly diagnosed HIV-1 cases among IDUs, but it is important that the RGD does not directly correspond to the number of infected individuals (2,38). According to our analyses using the skyline model, the local Finnish epidemic started with a sharp increase of RGD in 1998, followed by a short plateau and another increase in 2001 (Fig.…”
Section: Resultsmentioning
confidence: 87%
“…However, for both the Swedish and Finnish data sets, the epidemic dynamics shown by the above ML analyses were also captured by Bayesian analyses, using a relaxed clock and two different growth models (the nonparametric skyline growth model and the logistic growth model). This allowed us to infer when epidemic events occurred ( This coincides with the increase in newly diagnosed HIV-1 cases among IDUs, but it is important that the RGD does not directly correspond to the number of infected individuals (2,38). According to our analyses using the skyline model, the local Finnish epidemic started with a sharp increase of RGD in 1998, followed by a short plateau and another increase in 2001 (Fig.…”
Section: Resultsmentioning
confidence: 87%
“…More recently they have allowed estimates to be made of the origins of diverse epidemics in different countries and risk groups Salemi et al 2008). Finally, in combination with very large data sets, these approaches have allowed a bridge to be made across to infectious disease epidemiology, as under certain assumptions, the viral evolutionary history can be used to estimate critical epidemiological parameters that are not accessible from other routes (Volz et al 2009). …”
Section: Overview Of Virus Evolution and Rates Of Changementioning
confidence: 99%
“…[1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20] However, there is confusion surrounding HIV clustering due to differences in sampling, methodological approaches, and interpretation of HIV clustering results across studies. Issues that still need to be resolved through dedicated studies, meta-analyses, and comprehensive reviews include the following: What is the definition of an HIV cluster?…”
Section: Introductionmentioning
confidence: 99%