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[Preprint]. 2025 May 29:2025.05.28.25328475.
doi: 10.1101/2025.05.28.25328475.

Shifting Dynamics of DENV2 in Costa Rica: Emergence of the Cosmopolitan Genotype (2024)

Mauricio Gonzalez Elizondo  1 , Dihala Picado Soto  1 , Estela Cordero Laurent  1 , Francisco Duarte Martínez  1 , Luiz Carlos Junior Alcantara  2 , Vagner Fonseca  3 , Jairo Andrés Méndez Rico  4 , Jose Lourenco  5 , Leticia Franco  4 , Marta Giovanetti  6   7 , Claudio Soto Garita  1
Affiliations

Shifting Dynamics of DENV2 in Costa Rica: Emergence of the Cosmopolitan Genotype (2024)

Mauricio Gonzalez Elizondo et al. medRxiv. .

Update in

Abstract

Dengue remains a major public health challenge. In Costa Rica, we implemented the first nationwide genomic surveillance to track the emergence of the DENV2 Cosmopolitan genotype. Phylogenetic and eco-epidemiological analyses revealed early detection, climate-linked spread, and spatial heterogeneity. Findings underscore the need for integrated surveillance to guide adaptive responses to emerging arboviral threats.

Keywords: Cosmopolitan genotype; Costa Rica; Dengue virus; eco-epidemiological modelling; genomic monitoring.

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Figures

Figure 1.
Figure 1.. Temporal and spatial correlation between climate-driven suitability and dengue incidence in Costa Rica.
a) Time series of monthly dengue cases (black line, right axis) and climate-driven suitability index for transmission (blue line, left axis) from June 2014 to November 2024. Shaded area (yellow) indicates the epidemic period during which enough cases with a clear seasonal signal are reported allowing to estimate correlation (Spearman’s test, r = 0.38, p-value<0.05) between suitability and incidence; b–c) Province-level correlation ((Spearman’s test) between monthly dengue incidence and climate suitability for the years 2022 (b) and 2023 (c). Warmer colors indicate stronger correlations. Dashed boundaries (white) mark provinces with non-significant correlation (p-value>0.05) and solid boundaries (dark grey) otherwise. In 2023, higher correlations were observed in eastern and coastal provinces where early cases of the DENV2 Cosmopolitan genotype were detected.
Figure 2.
Figure 2.. Dengue Serotype Dynamics in Costa Rica.
a) Proportional distribution of DENV serotypes over time; b) Age of dengue cases over time (left) and by number of circulating serotypes (right). Median (red), interquartile range (dark gray), and standard deviation (light gray) are shown; c) Geographic distribution of DENV2 genotypes in Costa Rica from May 2023 to August 2024.
Figure 3.
Figure 3.. Evolutionary and spatiotemporal expansion of DENV2-III in Costa Rica.
a) Maximum likelihood (ML) phylogeny of DENV2-III, showing Costa Rican sequences (red) within the broader Central and South American clade. Phylogenetic support is indicated at key nodes; b) ML reconstruction of DENV2-III lineage D.1.2 dispersal within Costa Rica; c) Population density map of Costa Rica, highlighting areas with elevated transmission potential; d, e) Spatiotemporal expansion of DENV-2 III lineage D.1.2, illustrating the progressive spread of two distinct clades—Clade I and II—from urban centers to coastal regions between May 2023 and March 2024.
Figure 4.
Figure 4.. Emergence and spread of DENV2-II in Costa Rica.
a) Maximum likelihood (ML) phylogeny of DENV2-II, highlighting the American clade. The inset on the right displays the time-stamped phylogenetic tree, showing two independent introductions of this genotype into Costa Rica, including one major transmission cluster. Tips are colored according to sampling location; b) Time-scaled phylogenetic reconstruction of the major DENV2-II clade, illustrating its expansion from Puntarenas, Limón, and Cartago in early 2024; c) Spatiotemporal dynamics of the major DENV2-II clade in Costa Rica.
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References

    1. Pan-American Health Organization (PAHO), 2025. https://www.paho.org/en/documents/dengue-epidemiological-situation-regio...
    1. Nakase T., Giovanetti M., Obolski U. et al. Population at risk of dengue virus transmission has increased due to coupled climate factors and population growth. Commun Earth Environ 5, 475 (2024). 10.1038/s43247-024-01639-6 - DOI
    1. Ministerio de Salud Costa Rica. https://www.ministeriodesalud.go.cr/
    1. Pan-American Health Organization (PAHO), Dengue cases. https://www3.paho.org/data/index.php/en/mnu-topics/indicadores-dengue-en...
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