Genomic Characterization of Dengue virus 1 detected in Cabo Verde, 2024
Isaias Varela1, Kevin Carvalho1, Delissa de Pina1, Menilita Barbosa2, Leidiza Tavares2, Valdir Furtado2, Adelina Dias2, Moussa Moïse Diagne3, Idrissa Dieng3$, Maria da Luz Mendonça4$
1Genomic Sequencing and Bioinforatics Unity – National Public Health Institue, Praia, Cabo Verde.
2Virology laboratory - National Public Health Institue, Praia, Cabo Verde.
3Virology Department - Institut Pasteur de Dakar
4National Public Health Institue, Praia, Cabo Verde.
$Co-Last Author
Correspondence:
Dr Idrissa DIENG : [email protected]
Isaias Varela : [email protected]
Background
Arboviruses as Dengue virus, Zika virus were reported among human population in Cabo Verde in the past (Alvarenga Varela, 2015; DePina et al., 2019). Since the period post Zika epidemic in 2016 any report of arboviruses circulation was described. In 2023 following the implementation of a syndromic surveillance program in the Archipelagos re-emergence of DENV-3 was reported (Santos et al., 2024). In January 2024 DENV-1 cases were detected in the Archipelagos herein we described the genomic characterization of circulating DENV-1 strains.
The Study
Using amplicon based tilling PCR followed by nanopore sequencing as previously described (Dieng et al., 2023) , 52 DENV-1 nearly complete genome was generated with genomic coverage > 80 % (Figure 1).
Figure 1. Coverage plot of generated 52 DENV-1 genomes from Cabo Verde
Geographically the highest number of generated genomes comes from Santiago (n = 50) and Fogo (n = 02).
Performed phylogenetic and Phylogeographic analysis using nextstrain (Figure 2) shows that the DENV-1 epidemic was driven by the 1III_A.2 lineage. Interestingly this lineage was known to be circulating in West Africa and associated to outbreak in Mali, Togo, Senegal in 2022, 2023 and 2025 respectively (Dieng et al., 2024, 2025; Kane et al., 2025).
Figure 2. Phylogeography of the DENV-1III_1.2 lineage detected in Cabo Verde showing and endemicity in West Africa and putative introduction from Mali
Conclusion
This study reports the first genomic characterization of a DENV-1 strain associated with a large outbreak in Cabo Verde, providing molecular evidence of autochthonous DENV-1 circulation in the country in 2024. Phylogenetic analysis revealed that the outbreak was driven by DENV-1 lineage 1III_A.2, a lineage previously documented in West Africa, suggesting endemic circulation across the region.
These findings underscore the critical role of sentinel syndromic surveillance programs in mitigating arbovirus burden in West Africa and in clarifying the contribution of dengue to non-malarial febrile illness. The real-time genomic characterization of circulating strains in Praia not only establishes a baseline for future genomic epidemiology studies in Cabo Verde but also provides actionable data to inform integrated prevention and control strategies.
References
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