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The European Physical Journal Special Topics

, Volume 222, Issue 6, pp 1347–1358 | Cite as

Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM

  • Rick QuaxEmail author
  • David A. M. C. van de Vijver
  • Dineke Frentz
  • Peter M. A. Sloot
Regular Article Simultaneous Dynamics ON and OF Networks

Abstract

The HIV-1 epidemic in Europe is primarily sustained by a dynamic topology of sexual interactions among MSM who have individual immune systems and behavior. This epidemiological process shapes the phylogeny of the virus population. Both fields of epidemic modeling and phylogenetics have a long history, however it remains difficult to use phylogenetic data to infer epidemiological parameters such as the structure of the sexual network and the per-act infectiousness. This is because phylogenetic data is necessarily incomplete and ambiguous. Here we show that the cluster-size distribution indeed contains information about epidemiological parameters using detailed numberical experiments. We simulate the HIV epidemic among MSM many times using the Monte Carlo method with all parameter values and their ranges taken from literature. For each simulation and the corresponding set of parameter values we calculate the likelihood of reproducing an observed cluster-size distribution. The result is an estimated likelihood distribution of all parameters from the phylogenetic data, in particular the structure of the sexual network, the per-act infectiousness, and the risk behavior reduction upon diagnosis. These likelihood distributions encode the knowledge provided by the observed cluster-size distrbution, which we quantify using information theory. Our work suggests that the growing body of genetic data of patients can be exploited to understand the underlying epidemiological process.

Keywords

European Physical Journal Special Topic Recent Common Ancestor Infection Event Phylogenetic Information Sexual Network 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© EDP Sciences and Springer 2013

Authors and Affiliations

  • Rick Quax
    • 1
    Email author
  • David A. M. C. van de Vijver
    • 2
  • Dineke Frentz
    • 2
  • Peter M. A. Sloot
    • 1
    • 3
    • 4
  1. 1.Computational ScienceUniversity of AmsterdamAmsterdamThe Netherlands
  2. 2.Department of Virology, Erasmus Medical CentreErasmus UniversityRotterdamThe Netherlands
  3. 3.National Research University of Information Technologies, Mechanics and Optics (ITMO)Saint PetersburgRussia
  4. 4.Nanyang Technological UniversitySingaporeSingapore

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