Inferring Epidemic Contact Structure from Phylogenetic Trees
| Autor: | Cristina Cellerai, Viktor von Wyl, Thomas Klimkait, Huldrych F. Günthard, Tanja Stadler, Roger D. Kouyos, Jürg Böni, Gabriel E. Leventhal, Sabine Yerly, Sebastian Bonhoeffer |
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| Přispěvatelé: | University of Zurich |
| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Male
0106 biological sciences 10028 Institute of Medical Virology Epidemiology Disease Transmission Infectious/statistics & numerical data 2804 Cellular and Molecular Neuroscience Population Modeling HIV Infections 01 natural sciences 10234 Clinic for Infectious Diseases Switzerland/epidemiology Risk Factors Statistics Prevalence Biology (General) Phylogeny Contact Tracing/methods ddc:616 Genetics 0303 health sciences education.field_of_study Ecology Phylogenetic tree Spatial epidemiology Genetic Predisposition to Disease/epidemiology/genetics Tree (data structure) Infectious Diseases Computational Theory and Mathematics Modeling and Simulation Medicine Female Switzerland Research Article Network analysis QH301-705.5 Population Structure (category theory) 610 Medicine & health Biology Risk Assessment 010603 evolutionary biology 03 medical and health sciences Cellular and Molecular Neuroscience 1311 Genetics Disease Transmission Infectious 1312 Molecular Biology Humans Genetic Predisposition to Disease Risk Assessment/methods education Molecular Biology Ecology Evolution Behavior and Systematics Proportional Hazards Models 030304 developmental biology Population Biology Null model Computational Biology 1105 Ecology Evolution Behavior and Systematics HIV Infections/epidemiology/genetics 570 Life sciences biology Contact Tracing 2303 Ecology Contact tracing 2611 Modeling and Simulation 1703 Computational Theory and Mathematics |
| Zdroj: | PLoS Computational Biology; Vol 8 PLoS Computational Biology, 8 (3) PLoS computational biology PLoS Computational Biology Plos Computational Biology, vol. 8, no. 3, pp. e1002413 PLOS Computational Biology, Vol. 8, No 3 (2012) P. e1002413 PLoS Computational Biology, Vol 8, Iss 3, p e1002413 (2012) |
| ISSN: | 1553-7358 1553-734X |
| DOI: | 10.1371/journal.pcbi.1002413 |
| Popis: | 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. PLoS Computational Biology, 8 (3) ISSN:1553-734X ISSN:1553-7358 |
| Databáze: | OpenAIRE |
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