Phylogeography and Population Dynamics of Dengue Viruses in the Americas

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.

Phylogenetic Patterns of Human Coxsackievirus B5 Arise from Population Dynamics between Two Genogroups and Reveal Evolutionary Factors of Molecular Adaptation and Transmission

“…For instance, the EV report for the United States indicated a singular CVB5 epidemic pattern with sharp increases at 3-to 6-year intervals. Our data also emphasize the ability of coalescence-based models (41) to depict the complex epidemic patterns of EV infections from genetic data, as reported earlier for other widespread RNA viruses (58).…”

Population dynamics of DENV-1 genotype V in Brazil is characterized by co-circulation and strain/lineage replacement

“…This was particularly evident for L3, L6, L1a, L1b, L6-BR and isolates within L6-BR obtained in the Southeast Region of Brazil. This pattern is similar to the pattern observed by Allicock et al [51], who demonstrated that the MRCAs of all DENV serotypes were estimated to exist for several years (between 2 and 4 years, or 2 years in the case of DENV-1) prior to the first reported outbreaks for each serotype. These findings can be explained by the possibility of viruses remaining undetected until a threshold number of infections/disease incidences is reached that can be detected by the limited surveillance systems of most countries in the Americas [51].…”

Arboviruses: Variations on an Ancient Theme

“…Indeed, mean substitution rates for the four DENV serotypes ranging from 7.8 × 10 -4 to 9.9 × 10 -4 substitutions/site have been reported by Allicock et al [129], and comparable values have also been obtained in previous studies [128,130]. This considerable diversity is illustrated by the fact that several genotypes (with unique genetic future science group www.futuremedicine.com signatures) are currently defined for all existing DENV serotypes, and interactions and competition between these different genotypes may have serious epidemiological implications.…”