First whole-genome detection of dengue virus in urban Aedes aegypti from Southern Brazil

TL;DR

This study reports the first detection of dengue virus in mosquitoes from southern Brazil, revealing co-circulating strains and signs of viral adaptation.

Contribution

The first whole-genome detection of dengue virus in urban Aedes aegypti mosquitoes from southern Brazil using vector-based genomic surveillance.

Findings

DENV-1 (Genotype V) and DENV-2 (Genotype II) were detected in mosquitoes, with evidence of co-circulation.

Phylogenetic analysis showed sustained local transmission and multiple viral introductions.

Recurrent mutations in non-structural proteins suggest ongoing viral adaptation.

Abstract

Dengue virus (DENV) is a major global health threat whose expansion into temperate regions has been facilitated by climate change and vector adaptation. Despite recurrent epidemics in Brazil, genomic surveillance in mosquito vectors remains limited, particularly in southern regions, constraining our understanding of local transmission dynamics and viral evolution. Here, we aimed to investigate dengue virus circulation, serotype co-circulation, and genomic signals of viral adaptation through vector-based genomic surveillance in southern Brazil. Using this approach, we provide genomic evidence of dengue virus circulation in southern Brazil during 2023. Whole-genome sequencing revealed active circulation of both DENV-1 (Genotype V) and DENV-2 (Genotype II), with the detection of mosquito pools harboring both serotypes, indicating their simultaneous circulation and raising concerns about increased transmission complexity and sequential infection risk in humans. Phylogenetic analyses supported sustained local transmission alongside multiple viral introductions. Moreover, recurrent mutations, particularly in non-structural proteins (NS1, NS2A, and NS5), suggest ongoing viral adaptation. These findings represent the first vector-derived genomic data for dengue in southern Brazil and highlight the critical role of mosquito-based genomic surveillance in detecting co-circulating serotypes, monitoring viral evolution, and strengthening preparedness in emerging transmission settings.

Dengue virus (DENV) continues to expand into new regions, driven by climate change and mosquito adaptation. In Brazil, dengue epidemics are recurrent, but genomic surveillance of mosquitoes is still scarce, particularly in the southern states. To fill this gap, we implemented an urban mosquito-trapping strategy designed for low-density and peri-domestic environments in Porto Alegre, Rio Grande do Sul. From April to July 2023, we collected 4,768 Aedes aegypti samples across 16 neighborhoods, generating 2,022 pools. Among these, 41 pools tested positive for DENV, of which 33 pools exhibited RNA integrity suitable for sequencing. The analysis revealed circulation of DENV-1 (Genotype V) and DENV-2 (Genotype II), with two pools showing co-circulation of both serotypes, raising concern for sequential infections in humans. Phylogenetic analysis revealed sustained local transmission combined with multiple virus introductions, and mutations in viral proteins suggested ongoing viral adaptation. Our findings provide the first mosquito-based genomic data for dengue in southern Brazil and highlight how mosquito genomics can strengthen early outbreak detection, serotype monitoring, and epidemic preparedness.

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