Regional Structuring of Aedes Aegypti Maternal Lineages and Detection of Insect-Specific Flaviviruses in Kenya

Dengue virus (DENV) is an expanding global health threat, yet its ecological and entomological drivers remain poorly defined in sub-Saharan Africa. In Kenya, recurrent outbreaks along the coastal region contrast sharply with the persistent absence of outbreaks in ecologically suitable western Kenya. Understanding the spatial heterogeneity of vector populations, viral circulation, and ecological context is essential for identifying under-recognized determinants of dengue emergence. We conducted a comparative entomological and virological survey across outbreak-prone coastal Kenya and the low-outbreak but dengue-reporting region of western Kenya. Mosquito community composition and blood-feeding patterns were quantified. Ae. aegypti populations were genetically profiled using mitochondrial cytochrome oxidase subunit I (COI) haplotypes. Although proportional Ae. aegypti abundance was lower along the coast, three insect-specific flavivirus (ISFV)-positive mosquitoes-including two males-were detected in this region, indicating localized circulation and probable vertical transmission. No DENV-positive mosquitoes were detected in either region despite higher adult Ae. aegypti abundance in western Kenya. COI haplotyping revealed a shallow but structured mosaic of maternal lineages among the sampled Kenyan regions, with private coastal haplotypes and elevated diversity in Busia, suggesting distinct evolutionary histories and limited but ongoing gene flow. Kenyan ISFVs clustered within a globally distributed Ae. aegypti-associated lineage. The exclusive detection of ISFVs during peak mosquito activity underscores the complexity of Kenya's vector-virus ecology and highlights the ability of coastal Ae. aegypti to sustain vertically transmitted viruses. These findings support the need for region-specific, ecology-informed surveillance frameworks integrating vector genetics, virome composition, and environmental context to better anticipate dengue emergence in Africa.