Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing t...

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Vydáno v:Molecular biology and evolution Ročník 33; číslo 8; s. 2102 - 2116
Hlavní autoři: Kühnert, Denise, Stadler, Tanja, Vaughan, Timothy G., Drummond, Alexei J.
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Society for Molecular Biology and Evolution 01.08.2016
Oxford University Press
Témata:
Bayes Theorem
Computer Simulation
Disease Outbreaks
Epidemics
Genomics - methods
Humans
Influenza A Virus, H3N2 Subtype - genetics
Influenza A Virus, H3N2 Subtype - isolation & purification
Influenza, Human - epidemiology
Influenza, Human - transmission
Influenza, Human - virology
Methods
Phylogeny
Phylogeography - methods
epidemiology
Bayesian inference
biogeography
birth-death model
infectious diseases
phylogeography
ISSN:0737-4038, 1537-1719, 1537-1719
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Shrnutí:When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth–death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters.We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group.
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Associate editor: Jeffrey Thorne
ISSN:0737-4038
1537-1719
1537-1719
DOI:10.1093/molbev/msw064