Metagenomic Analysis of the RNA Metavirome of Aedes aegypti Mosquitoes Collected from Coastal Kenya

Abstract

The coastal region of Kenya has experienced repeated outbreaks of chikungunya (CHIKV) and dengue (DENV) viruses transmitted by local populations of the Aedes aegypti mosquito. In addition, this mosquito has been reported to harbor insect specific viruses (ISVs), some of which can either enhance or suppress arboviral transmission. Despite the arboviral burden in coastal Kenya, there has been no systematic molecular entomological surveillance in this region and the viral diversity of local Aedes aegypti populations remains largely unknown. To understand the Aedes aegypti virome from coastal Kenya sampled outside outbreaks, this study conducted a retrospective study of mosquitoes collected during a sectional survey to determine their urban ecology. Adult mosquitoes were lured using Biogent’s sentinel traps at 16 different localities along the Kenyan coast between May to September 2017. Pools of 20 female Aedes aegypti mosquitoes were generated following grouping by morphological characteristics. Presence of arboviruses in the mosquito pools was determined using virus-specific and genera-specific primers on the real-time PCR. Metagenomic next generation sequencing (mNGS) on Illumina Miseq and analysis was used to characterize the virome. A total of 16,520 female Aedes aegypti grouped into 826 pools were analyzed. Flaviviruses were detected in 69/826 (8.4%) pools by real time PCR. Sequencing generated 8,459/971,754 (0.87%) clean reads that were taxonomically assigned to 16 and 28 viral families and species, respectively. The family Phenuiviridae represented by Phasi Charoen-like phasivirus (PCLV) species was the most abundant, detected in 64/73 (87%) mosquito pools. No pathogenic viruses were identified by mNGS. Phylogenetic analysis revealed local PCLV and Cell fusing agent virus (CFAV) were distinct from global sequences. Our data provides information about virus diversity and composition of the Aedes aegypti mosquitoes from coastal Kenya and contributes to the body knowledge of Aedes aegypti virome. To the best of our knowledge, this is the first study to provide this information from this region. Future studies should sample longitudinally across the country or region during and between arboviral outbreaks so as to gain understanding of the temporal viral diversity in local or regional Aedes aegypti populations.