Dengue Virus Serotype 3 Origins and Genetic Dynamics, Jamaica

Abstract

We identified 3 clades of dengue virus serotype 3 belonging to genotype III isolated during 2019-2020 in Jamaica by using whole-genome sequencing and phylogenomic and phylogeographic analyses. The viruses likely originated from Asia in 2014. Newly expanded molecular surveillance efforts in Jamaica will guide appropriate public health responses.

Keywords: Caribbean; Jamaica; dengue; dengue virus; dengue virus serotype 3; genotype; sequence; serotype; vector-borne infections; viruses; zoonoses.

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.

Figure 2

Time-scaled explicit discrete phylogeographic analysis of dengue virus serotype 3 (DENV-3) spread in Jamaica. Relationship between the dispersal trajectory of DENV-3 in the maximum clade credibility tree and the specific DENV-3 migration patterns into Jamaica over time (box) is indicated. Nodes of the tree represent the inferred country of origin for sampled strains. Arrows indicate the nodes from which taxa were selected for analysis by using the TaxaMarkovJumpHistoryAnalyzer (https://github.com/beast-dev/beast-mcmc). Only values of discrete state probability for the root and the node of interest are shown in the tree; complete state probability values of the nodes are indicated in Appendix Figure 2, panel B. Dynamic pathways of DENV-3 geographic movement are indicated by Markov jump mappings (right circular map). Transmission network of DENV-3 is summarized by Markov jump events, analyzed using TreeMarkovJumpHistoryAnalyzer and visualized in a circular layout by using the circlize package in R (The R Project for Statistical Computing, https://www.r-project.org). The width of each link reflects the frequency of virus movement; quantitative estimates were provided by using the TreeMarkovJumpHistoryAnalyzer. Tick marks on the outside of the circle’s segments indicate virus movement frequencies.

Figure 3

Time-scaled phylogenetic analysis, molecular characterization, dynamics, and natural selection of dengue virus serotype 3 in Jamaica. A) Phylogenetic tree indicates monophyletic clusters of strains from Jamaica (bold text) extracted from the discrete phylogeographic analysis (Figure 2). Discrete sp values (ω) for nodes evaluated for episodic selection are shown. Full sp values for nodes are shown in Appendix Figure 2, panel B. B) Strains were evaluated for amino acid replacements according to each TG. Arrows indicate episodic selection of each main TG clade. Bold text indicates positively selected mutations. sp, state probability; TG, temporal group.

Figure 4

Envelope glycoprotein 3-dimensional structures (structure 7a3s; RCSB Protein Data Bank, https://www.rcsb.org) from dengue virus serotype 3 strains in Jamaica. Red indicates protein domain I, yellow indicates domain II, and blue indicates domain III. Gray spheres indicate mutations identified across various TGs. Arrows indicate mutations detected by site models. E621Q (faded text) is in the loop region not visible in the crystal structure. TG, temporal group.