Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model

The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiologi...

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Vydáno v:Journal of the Royal Society interface Ročník 11; číslo 94; s. 20131106
Hlavní autoři: Kühnert, Denise, Stadler, Tanja, Vaughan, Timothy G, Drummond, Alexei J
Médium: Journal Article
Jazyk:angličtina
Vydáno: England 06.05.2014
Témata:
Argentina - epidemiology
Genotype
Hepacivirus - genetics
Hepatitis C - epidemiology
Hepatitis C - genetics
HIV Infections - epidemiology
HIV Infections - genetics
HIV-1 - immunology
Humans
Models, Biological
Phylogeny
United Kingdom - epidemiology
mathematical epidemiology
Bayesian phylogenetics
birth–death prior
phylodynamics
ISSN:1742-5662, 1742-5662
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Shrnutí:The evolution of RNA viruses, such as human immunodeficiency virus (HIV), hepatitis C virus and influenza virus, occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible-infected-removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our birth-death SIR method to two viral datasets. First, five HIV type 1 clusters sampled in the UK between 1999 and 2003 are analysed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 1990s. The analysis of a hepatitis C virus genotype 2c dataset shows that the local epidemic in the Córdoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880 to 1920. The estimated time of epidemic peak is around 1970.
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ISSN:1742-5662
1742-5662
DOI:10.1098/rsif.2013.1106