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. 2010 Jul 27;4(7):e766.
doi: 10.1371/journal.pntd.0000766.

Phylogeography of recently emerged DENV-2 in southern Viet Nam

Maia A Rabaa  1 , Vu Thi Ty Hang, Bridget Wills, Jeremy Farrar, Cameron P Simmons, Edward C Holmes
Affiliations

Phylogeography of recently emerged DENV-2 in southern Viet Nam

Maia A Rabaa et al. PLoS Negl Trop Dis. .

Abstract

Revealing the dispersal of dengue viruses (DENV) in time and space is central to understanding their epidemiology. However, the processes that shape DENV transmission patterns at the scale of local populations are not well understood, particularly the impact of such factors as human population movement and urbanization. Herein, we investigated trends in the spatial dynamics of DENV-2 transmission in the highly endemic setting of southern Viet Nam. Through a phylogeographic analysis of 168 full-length DENV-2 genome sequences obtained from hospitalized dengue cases from 10 provinces in southern Viet Nam, we reveal substantial genetic diversity in both urban and rural areas, with multiple lineages identified in individual provinces within a single season, and indicative of frequent viral migration among communities. Focusing on the recently introduced Asian I genotype, we observed particularly high rates of viral exchange between adjacent geographic areas, and between Ho Chi Minh City, the primary urban center of this region, and populations across southern Viet Nam. Within Ho Chi Minh City, patterns of DENV movement appear consistent with a gravity model of virus dispersal, with viruses traveling across a gradient of population density. Overall, our analysis suggests that Ho Chi Minh City may act as a source population for the dispersal of DENV across southern Viet Nam, and provides further evidence that urban areas of Southeast Asia play a primary role in DENV transmission. However, these data also indicate that more rural areas are also capable of maintaining virus populations and hence fueling DENV evolution over multiple seasons.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. MCC phylogeny of the DENV-2 Asian I genotype in southern Viet Nam (2003–2008) according to province of sampling.
Tips are colored by province of sampling. Internal branches are colored based on the reconstructed ancestral state as estimated by the reversible diffusion model. Branches colored black indicate Bayesian posterior probabilities less than 0.85. Estimated support for the reconstructed ancestral state is indicated by open (>95%) and closed (>85%) diamonds.
Figure 2
Figure 2. DENV-2 Asian I genotype dispersal across provinces of southern Viet Nam.
Map showing significant pathways of diffusion estimated between provinces of southern Viet Nam. Solid lines indicate diffusion pathways among provinces with a shared border. Dashed lines indicate diffusion pathways among provinces that do not have a shared border. Numbers in parentheses indicate the number of sequences included in each group.
Figure 3
Figure 3. MCC phylogeny of the DENV-2 Asian I genotype in southern Viet Nam (2003–2008) according to population density (within HCMC) or province of sampling.
Tips are colored by urban level (within HCMC) or province of sampling. Internal branches are colored based on the reconstructed ancestral state as estimated by the reversible diffusion model. Branches colored black indicate Bayesian posterior probabilities less than 0.85. Estimated support for the reconstructed ancestral state is indicated by open (>95%) and closed (>85%) diamonds.
Figure 4
Figure 4. DENV-2 Asian I genotype dispersal across a population density gradient in HCMC and southern Viet Nam.
Map showing significant pathways of diffusion estimated between three regions of gradated population density within HCMC and the remaining nine provinces of southern Viet Nam. Solid lines indicate diffusion pathways among regions with a shared border. Dashed lines indicate diffusion pathways among regions that do not have a shared border. Numbers in parentheses indicate the number of sequences included in each group.
Figure 5
Figure 5. DENV-2 Asian I genotype dispersal among districts of Ho Chi Minh City, Viet Nam.
Map indicating significant pathways of diffusion estimated between district groups within HCMC. Solid lines indicate diffusion pathways among areas with a shared border. Dashed lines indicate diffusion pathways among areas that do not have a shared border. Numbers in parentheses indicate the number of sequences included in each group.
Figure 6
Figure 6. DENV-2 Asian I genotype dispersal among districts of Ho Chi Minh City and provinces of southern Viet Nam.
Map showing significant pathways of diffusion estimated between district groups within HCMC and provinces of southern Viet Nam. Solid lines indicate diffusion pathways among regions with a shared border. Dashed lines indicate diffusion pathways among regions that do not have a shared border. Numbers in parentheses indicate the number of sequences included in each group.
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