Shifting Dynamics of Dengue Virus Serotype 2 and Emergence of Cosmopolitan Genotype, Costa Rica, 2024

Abstract

Dengue remains a major public health challenge. In Costa Rica, we implemented nationwide genomic surveillance to track dengue virus serotype 2 cosmopolitan genotype emergence. Phylogenetic and eco-epidemiologic analyses revealed early detection, climate-driven spread, and spatial heterogeneity. Our findings underscore the need for integrated surveillance to guide adaptive responses to emerging arboviral threats.

Keywords: Costa Rica; Dengue virus; cosmopolitan genotype; dengue; eco-epidemiological modelling; genomic monitoring; mosquitoborne infections; vector-borne infections; viruses.

Figure 1

Temporal and spatial correlation between climate-driven suitability and dengue incidence from a study of shifting dynamics of dengue virus serotype 2 and emergence of cosmopolitan genotype, Costa Rica, 2024. A) Time series of monthly dengue cases and climate-driven suitability index for transmission during June 2014–November 2024. Shaded area (yellow) indicates the epidemic period during which enough cases with a clear seasonal signal were reported to enable an estimate correlation between suitability and incidence (Spearman r = 0.38; p<0.05). Scale bars for the y-axes differ substantially to underscore patterns. B, C) Province-level Spearman correlation values between monthly dengue incidence and climate suitability during 2022 (B) and 2023 (C). Warmer colors indicate stronger correlations. White dashed boundaries mark provinces with nonsignificant correlation (p>0.05) and solid dark gray boundaries indicate provinces with statistically significant correlation. In 2023, higher correlations were observed in eastern and coastal provinces where early cases of the dengue virus serotype 2 cosmopolitan genotype were detected.

Figure 2

Maximum-likelihood phylogeny and spatiotemporal expansion of dengue virus (DENV) serotype 2 (DENV-2) and emergence of cosmopolitan genotype, Costa Rica, 2024. A) Time-stamped phylogenetic tree of DENV-2 genotype III, showing 2 independent introductions of this genotype into Costa Rica, including 1 major transmission cluster. Tips are colored according to sampling location. Scale bar indicates nucleotide substitutions per site. Full phylogeny shown in Appendix 1 Figure. B) Population density map of Costa Rica, highlighting areas with elevated DENV transmission potential. C, D) Spatiotemporal expansion of DENV-2 genotype III lineage D.1.2, illustrating the progressive spread of 2 distinct clades, clade I (C) and clade II (D), from urban centers to coastal regions between May 2023 and March 2024.

Figure 3

Time-scaled and spatiotemporal dynamics of dengue virus serotype 2 (DENV-2) and emergence of cosmopolitan genotype, Costa Rica, 2024. A) Time-scaled phylogenic reconstruction of global DENV-2 showing major clade in Costa Rica in 2024. Full phylogeny shown in Appendix 1 Figure. B) Time-scaled phylogenetic reconstruction of the major DENV-2 genotype II clade, illustrating its expansion from Puntarenas, Limón, and Cartago in early 2024 (map inset). C) Spatiotemporal dynamics of the major DENV-2 genotype II clade in Costa Rica demonstrating its spread among provinces. DENV, dengue virus.