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Inferring epidemic contact structure from phylogenetic trees

Leventhal, Gabriel E
Kouyos, Roger
Stadler, Tanja
Wyl, Viktor von
Böni, Jürg
Cellerai, Cristina
Klimkait, Thomas
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Published in PLoS computational biology. 2012, vol. 8, no. 3, e1002413
Abstract Contact structure is believed to have a large impact on epidemic spreading and consequently using networks to model such contact structure continues to gain interest in epidemiology. However, detailed knowledge of the exact contact structure underlying real epidemics is limited. Here we address the question whether the structure of the contact network leaves a detectable genetic fingerprint in the pathogen population. To this end we compare phylogenies generated by disease outbreaks in simulated populations with different types of contact networks. We find that the shape of these phylogenies strongly depends on contact structure. In particular, measures of tree imbalance allow us to quantify to what extent the contact structure underlying an epidemic deviates from a null model contact network and illustrate this in the case of random mixing. Using a phylogeny from the Swiss HIV epidemic, we show that this epidemic has a significantly more unbalanced tree than would be expected from random mixing.
Keywords Contact Tracing/methodsDisease Transmission, Infectious/statistics & numerical dataFemaleGenetic Predisposition to Disease/epidemiology/geneticsHIV Infections/epidemiology/geneticsHumansMalePhylogenyPrevalenceProportional Hazards ModelsRisk Assessment/methodsRisk FactorsSwitzerland/epidemiology
PMID: 22412361
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Research group Groupe Laurent Kaiser (virologie clinique) (668)
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LEVENTHAL, Gabriel E et al. Inferring epidemic contact structure from phylogenetic trees. In: PLoS computational biology, 2012, vol. 8, n° 3, p. e1002413. doi: 10.1371/journal.pcbi.1002413 https://archive-ouverte.unige.ch/unige:74521

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Deposited on : 2015-08-06

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