Inferring epidemic contact structure from phylogenetic trees.

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...

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Autores principales:	Gabriel E Leventhal, Roger Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F Günthard, Sebastian Bonhoeffer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/e7921c13289d44fca8d68e80df4d2421
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id	oai:doaj.org-article:e7921c13289d44fca8d68e80df4d2421
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spelling	oai:doaj.org-article:e7921c13289d44fca8d68e80df4d24212021-11-18T05:51:31ZInferring epidemic contact structure from phylogenetic trees.1553-734X1553-735810.1371/journal.pcbi.1002413https://doaj.org/article/e7921c13289d44fca8d68e80df4d24212012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22412361/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Contact 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.Gabriel E LeventhalRoger KouyosTanja StadlerViktor von WylSabine YerlyJürg BöniCristina CelleraiThomas KlimkaitHuldrych F GünthardSebastian BonhoefferPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 3, p e1002413 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Gabriel E Leventhal Roger Kouyos Tanja Stadler Viktor von Wyl Sabine Yerly Jürg Böni Cristina Cellerai Thomas Klimkait Huldrych F Günthard Sebastian Bonhoeffer Inferring epidemic contact structure from phylogenetic trees.
description	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.
format	article
author	Gabriel E Leventhal Roger Kouyos Tanja Stadler Viktor von Wyl Sabine Yerly Jürg Böni Cristina Cellerai Thomas Klimkait Huldrych F Günthard Sebastian Bonhoeffer
author_facet	Gabriel E Leventhal Roger Kouyos Tanja Stadler Viktor von Wyl Sabine Yerly Jürg Böni Cristina Cellerai Thomas Klimkait Huldrych F Günthard Sebastian Bonhoeffer
author_sort	Gabriel E Leventhal
title	Inferring epidemic contact structure from phylogenetic trees.
title_short	Inferring epidemic contact structure from phylogenetic trees.
title_full	Inferring epidemic contact structure from phylogenetic trees.
title_fullStr	Inferring epidemic contact structure from phylogenetic trees.
title_full_unstemmed	Inferring epidemic contact structure from phylogenetic trees.
title_sort	inferring epidemic contact structure from phylogenetic trees.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/e7921c13289d44fca8d68e80df4d2421
work_keys_str_mv	AT gabrieleleventhal inferringepidemiccontactstructurefromphylogenetictrees AT rogerkouyos inferringepidemiccontactstructurefromphylogenetictrees AT tanjastadler inferringepidemiccontactstructurefromphylogenetictrees AT viktorvonwyl inferringepidemiccontactstructurefromphylogenetictrees AT sabineyerly inferringepidemiccontactstructurefromphylogenetictrees AT jurgboni inferringepidemiccontactstructurefromphylogenetictrees AT cristinacellerai inferringepidemiccontactstructurefromphylogenetictrees AT thomasklimkait inferringepidemiccontactstructurefromphylogenetictrees AT huldrychfgunthard inferringepidemiccontactstructurefromphylogenetictrees AT sebastianbonhoeffer inferringepidemiccontactstructurefromphylogenetictrees
_version_	1718424762615595008

Inferring epidemic contact structure from phylogenetic trees.

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