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Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data

BACKGROUND: Phylogenetic analysis is now an important tool in the study of viral outbreaks. It can reconstruct epidemic history when surveillance epidemiology data are sparse, and can indicate transmission linkages among infections that may not otherwise be evident. However, a remaining challenge is...

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Autores principales: Dellicour, Simon, Rose, Rebecca, Pybus, Oliver G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750353/
https://www.ncbi.nlm.nih.gov/pubmed/26864798
http://dx.doi.org/10.1186/s12859-016-0924-x
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author Dellicour, Simon
Rose, Rebecca
Pybus, Oliver G.
author_facet Dellicour, Simon
Rose, Rebecca
Pybus, Oliver G.
author_sort Dellicour, Simon
collection PubMed
description BACKGROUND: Phylogenetic analysis is now an important tool in the study of viral outbreaks. It can reconstruct epidemic history when surveillance epidemiology data are sparse, and can indicate transmission linkages among infections that may not otherwise be evident. However, a remaining challenge is to develop an analytical framework that can test hypotheses about the effect of environmental variables on pathogen spatial spread. Recent phylogeographic approaches can reconstruct the history of virus dispersal from sampled viral genomes and infer the locations of ancestral infections. Such methods provide a unique source of spatio-temporal information, and are exploited here. RESULTS: We present and apply a new statistical framework that combines genomic and geographic data to test the impact of environmental variables on the mode and tempo of pathogen dispersal during emerging epidemics. First, the spatial history of an emerging pathogen is estimated using standard phylogeographic methods. The inferred dispersal path for each phylogenetic lineage is then assigned a “weight” using environmental data (e.g. altitude, land cover). Next, tests measure the association between each environmental variable and lineage movement. A randomisation procedure is used to assess statistical confidence and we validate this approach using simulated data. We apply our new framework to a set of gene sequences from an epidemic of rabies virus in North American raccoons. We test the impact of six different environmental variables on this epidemic and demonstrate that elevation is associated with a slower rabies spread in a natural population. CONCLUSION: This study shows that it is possible to integrate genomic and environmental data in order to test hypotheses concerning the mode and tempo of virus dispersal during emerging epidemics. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-0924-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-47503532016-02-12 Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data Dellicour, Simon Rose, Rebecca Pybus, Oliver G. BMC Bioinformatics Methodology Article BACKGROUND: Phylogenetic analysis is now an important tool in the study of viral outbreaks. It can reconstruct epidemic history when surveillance epidemiology data are sparse, and can indicate transmission linkages among infections that may not otherwise be evident. However, a remaining challenge is to develop an analytical framework that can test hypotheses about the effect of environmental variables on pathogen spatial spread. Recent phylogeographic approaches can reconstruct the history of virus dispersal from sampled viral genomes and infer the locations of ancestral infections. Such methods provide a unique source of spatio-temporal information, and are exploited here. RESULTS: We present and apply a new statistical framework that combines genomic and geographic data to test the impact of environmental variables on the mode and tempo of pathogen dispersal during emerging epidemics. First, the spatial history of an emerging pathogen is estimated using standard phylogeographic methods. The inferred dispersal path for each phylogenetic lineage is then assigned a “weight” using environmental data (e.g. altitude, land cover). Next, tests measure the association between each environmental variable and lineage movement. A randomisation procedure is used to assess statistical confidence and we validate this approach using simulated data. We apply our new framework to a set of gene sequences from an epidemic of rabies virus in North American raccoons. We test the impact of six different environmental variables on this epidemic and demonstrate that elevation is associated with a slower rabies spread in a natural population. CONCLUSION: This study shows that it is possible to integrate genomic and environmental data in order to test hypotheses concerning the mode and tempo of virus dispersal during emerging epidemics. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-0924-x) contains supplementary material, which is available to authorized users. BioMed Central 2016-02-11 /pmc/articles/PMC4750353/ /pubmed/26864798 http://dx.doi.org/10.1186/s12859-016-0924-x Text en © Dellicour et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology Article
Dellicour, Simon
Rose, Rebecca
Pybus, Oliver G.
Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
title Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
title_full Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
title_fullStr Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
title_full_unstemmed Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
title_short Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
title_sort explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750353/
https://www.ncbi.nlm.nih.gov/pubmed/26864798
http://dx.doi.org/10.1186/s12859-016-0924-x
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