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. 2012 Jun;29(6):1533-43.
doi: 10.1093/molbev/msr320. Epub 2012 Jan 6.

Phylogeography and population dynamics of dengue viruses in the Americas

Orchid M Allicock  1 , Philippe Lemey, Andrew J Tatem, Oliver G Pybus, Shannon N Bennett, Brandi A Mueller, Marc A Suchard, Jerome E Foster, Andrew Rambaut, Christine V F Carrington
Affiliations

Phylogeography and population dynamics of dengue viruses in the Americas

Orchid M Allicock et al. Mol Biol Evol. 2012 Jun.

Abstract

Changes in Dengue virus (DENV) disease patterns in the Americas over recent decades have been attributed, at least in part, to repeated introduction of DENV strains from other regions, resulting in a shift from hypoendemicity to hyperendemicity. Using newly sequenced DENV-1 and DENV-3 envelope (E) gene isolates from 11 Caribbean countries, along with sequences available on GenBank, we sought to document the population genetic and spatiotemporal transmission histories of the four main invading DENV genotypes within the Americas and investigate factors that influence the rate and intensity of DENV transmission. For all genotypes, there was an initial invasion phase characterized by rapid increases in genetic diversity, which coincided with the first confirmed cases of each genotype in the region. Rapid geographic dispersal occurred upon each genotype's introduction, after which individual lineages were locally maintained, and gene flow was primarily observed among neighboring and nearby countries. There were, however, centers of viral diversity (Barbados, Puerto Rico, Colombia, Suriname, Venezuela, and Brazil) that were repeatedly involved in gene flow with more distant locations. For DENV-1 and DENV-2, we found that a "distance-informed" model, which posits that the intensity of virus movement between locations is inversely proportional to the distance between them, provided a better fit than a model assuming equal rates of movement between all pairs of countries. However, for DENV-3 and DENV-4, the more stochastic "equal rates" model was preferred.

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Figures

F<sc>ig.</sc> 1.
Fig. 1.
Timeline showing the introductions of the various genotypes of the four serotypes of DENV into the Americas. The flags of the countries associated with the first reports are displayed. BRA, Brazil; CUBA, Cuba; DOM, Dominica; JAM, Jamaica; NIC, Nicaragua; PAN, Panama; PR, Puerto Rico; and TRI, Trinidad and Tobago.
F<sc>IG</sc>. 2.
FIG. 2.
Demographic history of DENV-1 to DENV-4 (a–d) circulating in the Americas using Bayesian skyride model. The y axes of the skyline plots represent relative genetic diversity (Neτ). The x axis represents the number of years prior to the date of the most recent isolate in each analysis (i.e., 2007). The thick colored line is the mean estimate, and the 95% HPD are indicated by the shaded area. Below is a histogram (e) showing the percentage of infections confirmed by virus isolation for each serotype in each year.
F<sc>IG</sc>. 3.
FIG. 3.
Spatiotemporal dynamics of four DENV serotypes circulating in the Americas represented with snapshots of the dispersal pattern for January 1985, 1995, 2001, and 2008. Lines represent MCC phylogeny branches projected on the surface. The intensity of the color indicates the relative age of the dispersal pattern (darker = older).
F<sc>IG</sc>. 4.
FIG. 4.
Significant nonzero rates of movement for DENV-1 to DENV-4 (labeled a–d, respectively) as identified by Bayesian stochastic search variable selection using a BF test. Only links with BF > 6 are shown.
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