Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics
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Publication:2632857
DOI10.1016/J.JTBI.2014.02.031zbMATH Open1412.92221arXiv1306.3427OpenAlexW2963529202WikidataQ42225028 ScholiaQ42225028MaRDI QIDQ2632857FDOQ2632857
Authors: Amaury Lambert, H. K. Alexander, Tanja Stadler 
Publication date: 15 May 2019
Published in: Journal of Theoretical Biology (Search for Journal in Brave)
Abstract: The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge, none of the epidemiological models currently used in phylogenetics can account for recovery rates and sampling rates dependent on the time elapsed since transmission. Here we introduce an epidemiological model where infectives leave the epidemic, either by recovery or sampling, after some random time which may follow an arbitrary distribution. We derive an expression for the likelihood of the phylogenetic tree of sampled infectives under our general epidemiological model. The analytic concept developed in this paper will facilitate inference of past epidemiological dynamics and provide an analytical framework for performing very efficient simulations of phylogenetic trees under our model. The main idea of our analytic study is that the non-Markovian epidemiological model giving rise to phylogenetic trees growing vertically as time goes by, can be represented by a Markovian "coalescent point process" growing horizontally by the sequential addition of pairs of coalescence and sampling times. As examples, we discuss two special cases of our general model, namely an application to influenza and an application to HIV. Though phrased in epidemiological terms, our framework can also be used for instance to fit macroevolutionary models to phylogenies of extant and extinct species, accounting for general species lifetime distributions.
Full work available at URL: https://arxiv.org/abs/1306.3427
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Cites Work
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Cited In (9)
- On incomplete sampling under birth-death models and connections to the sampling-based coalescent
- Random ultrametric trees and applications
- The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes
- The probability distribution of the ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data
- Sampling-through-time in birth-death trees
- A stochastic model for the evolution of the influenza virus
- A Stochastic Model for Phylogenetic Trees
- Fitting Markovian binary trees using global and individual demographic data
- Estimating transmission from genetic and epidemiological data: a metric to compare transmission trees
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