Molecular Identification, Phylogeography and Genetic Diversity of Mosquitoes Collected from Areas Endemic to Rift Valley Fever in Kenya

Abstract

Rift Valley Fever virus is primarily transmitted by Aedes and Culex mosquitoes. The disease is zoonotic and is endemic in specific areas in Kenya. For a long time RVF mosquito vectors have been classified using morphological characteristics which have been found to be at times subjective and not very effective in classification. Molecular tools in use for mosquito classification such as Polymerase Chain Reaction- Restriction Fragment Length Polymorphism (PCR- RFLP) have also been reported to be cumbersome, thus more reliable and efficient tools are needed. In this study, validation of internal transcribed spacer (ITS) 1 and 2 as useful tools for molecular classification of mosquitoes was done and new molecular tools targeting intergenic/intronic loci were designed and tested for applicability in vector identification. The study was done using the 454 next generation sequencing of laboratory reared mosquitoes and mosquitos collected from different RVF endemic regions in Kenya. The ITS 1 region was highly divergent displaying a high degree of intraspecific and interspecific variation while the ITS 2 region was found to be highly conserved in the different species. These two loci would therefore not be appropriate tools for taxonomic and phylogeographic analysis of the vector populations. Three loci (ANG12432, ANG26425 and ANG20760) were found to be conserved within distinct genera with variation existing between genera making them appropriate for classification and accurate identification of mosquito species. In the study of population structure, none of the eleven sites used revealed distinct geographical distribution. ANG00020 loci separated samples obtained from the insectary and field samples suggesting applicability in distinguishing between laboratory reared and field collected mosquitoes, this observation requires validation.