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Volume 30, Number 10—October 2024
Dispatch
Dengue Virus Serotype 3 Origins and Genetic Dynamics, Jamaica
Figure 1
![Phylogenetic analysis, temporal emergence, and demographic characterization of DENV-3 in study of origins and genetic dynamics, Jamaica. A) Maximum-likelihood phylogenetic trees of global DENV-3 sequences indicate the strains circulating in Jamaica belong to genotype III and are organized into 3 independent clades (left tree). The sequences were mapped according to the country of sampling and their genotypes (right tree) by using the ggtreeExtra R package (The R Project for Statistical Computing, https://www.r-project.org). Bootstrap values >80% are displayed for all nodes in the left tree (colored circles at nodes) and only for external nodes and main clade of interest in the main tree (right side). All bootstrap values are shown in Appendix Figure 1. Scale bars indicate nucleotide substitutions per site. B) Time-scaled maximum clade credibility tree of DENV-3 sequences indicates the temporal emergence of DENV-3 strains in Jamaica starting in 2014. tMRCA and 95% HPD intervals for the tree root and the clade containing the sequences from Jamaica are indicated. Confidence values, determined by posterior probabilities, are indicated for external nodes and the node of interest. Full node support for the tree is indicated in Appendix Figure 2, panel A. Bayesian skygrid plot of the effective population size (Ne[τ]) over time indicates median values and 95% HPD intervals. DENV-3, dengue virus serotype 3; HPD, highest posterior density; tMRCA, time to most recent common ancestor.](/eid/images/24-0170-F1.jpg)
Figure 1. Phylogenetic analysis, temporal emergence, and demographic characterization of DENV-3 in study of origins and genetic dynamics, Jamaica. A) Maximum-likelihood phylogenetic trees of global DENV-3 sequences indicate the strains circulating in Jamaica belong to genotype III and are organized into 3 independent clades (left tree). The sequences were mapped according to the country of sampling and their genotypes (right tree) by using the ggtreeExtra R package (The R Project for Statistical Computing, https://www.r-project.org). Bootstrap values >80% are displayed for all nodes in the left tree (colored circles at nodes) and only for external nodes and main clade of interest in the main tree (right side). All bootstrap values are shown in Appendix Figure 1. Scale bars indicate nucleotide substitutions per site. B) Time-scaled maximum clade credibility tree of DENV-3 sequences indicates the temporal emergence of DENV-3 strains in Jamaica starting in 2014. tMRCA and 95% HPD intervals for the tree root and the clade containing the sequences from Jamaica are indicated. Confidence values, determined by posterior probabilities, are indicated for external nodes and the node of interest. Full node support for the tree is indicated in Appendix Figure 2, panel A. Bayesian skygrid plot of the effective population size (Ne[τ]) over time indicates median values and 95% HPD intervals. DENV-3, dengue virus serotype 3; HPD, highest posterior density; tMRCA, time to most recent common ancestor.
1These first authors contributed equally to this article.