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Literature DB >> 26139467

Getting to the root of epidemic spread with phylodynamic analysis of genomic data.

Abstract

When epidemiological and evolutionary dynamics occur on similar timescales, pathogen genomes sampled from infected hosts carry a signature of the dynamics of epidemic spread. Phylodynamic inference methods aim to extract this signature from genetic data. We discuss the contribution of phylodynamics toward understanding the 2014 West African Ebola virus epidemic.

Entities: Species

Keywords: Bayesian statistics; Ebola virus disease; MCMC; epidemiology; infectious diseases; phylogenetics

Mesh：

Year: 2015 PMID： 26139467 DOI： 10.1016/j.tim.2015.04.007

Source DB: PubMed Journal: Trends Microbiol ISSN： 0966-842X Impact factor: 17.079

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Cited

13 in total

1. Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

Authors: Sebastian Duchene; Remco Bouckaert; David A Duchene; Tanja Stadler; Alexei J Drummond
Journal: Syst Biol Date: 2019-03-01 Impact factor: 15.683

2. Markov genealogy processes.

Authors: Aaron A King; Qianying Lin; Edward L Ionides
Journal: Theor Popul Biol Date: 2021-12-09 Impact factor: 1.570

Review 3. Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications.

Authors: Leo A Featherstone; Joshua M Zhang; Timothy G Vaughan; Sebastian Duchene
Journal: Virus Evol Date: 2022-06-02

4. The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic.

Authors: Veronika Boskova; Tanja Stadler; Carsten Magnus
Journal: Virus Evol Date: 2018-01-29

5. Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

Authors: Sebastian Duchene; David A Duchene; Jemma L Geoghegan; Zoe A Dyson; Jane Hawkey; Kathryn E Holt
Journal: BMC Evol Biol Date: 2018-06-19 Impact factor: 3.260

6. Utilizing general human movement models to predict the spread of emerging infectious diseases in resource poor settings.

Authors: M U G Kraemer; N Golding; D Bisanzio; S Bhatt; D M Pigott; S E Ray; O J Brady; J S Brownstein; N R Faria; D A T Cummings; O G Pybus; D L Smith; A J Tatem; S I Hay; R C Reiner
Journal: Sci Rep Date: 2019-03-26 Impact factor: 4.379

Getting to the root of epidemic spread with phylodynamic analysis of genomic data.

1. Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

2. Markov genealogy processes.

Review 3. Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications.

4. The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic.

5. Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

6. Utilizing general human movement models to predict the spread of emerging infectious diseases in resource poor settings.

Review 7. Precision epidemiology for infectious disease control.

8. Unifying Phylogenetic Birth-Death Models in Epidemiology and Macroevolution.

9. Epidemiological dynamics of an urban Dengue 4 outbreak in São Paulo, Brazil.

10. Temporal signal and the phylodynamic threshold of SARS-CoV-2.