Population Genetics of Two Key Mosquito Vectors of Rift Valley Fever Virus Reveals New Insights into the Changing Disease Outbreak Patterns in Kenya

Rift Valley fever (RVF) outbreaks in Kenya have increased in frequency and range to include northeastern Kenya where viruses are increasingly being isolated from known (Aedes mcintoshi) and newly-associated (Ae. ochraceus) vectors. The factors contributing to these changing outbreak patterns are unclear and the population genetic structure of key vectors and/or specific virus-vector associations, in particular, are under-studied. By conducting mitochondrial and nuclear DNA analyses on >220 Kenyan specimens of Ae. mcintoshi and Ae. ochraceus, we uncovered high levels of vector complexity which may partly explain the disease outbreak pattern. Results indicate that Ae. mcintoshi consists of a species complex with one of the member species being unique to the newly-established RVF outbreak-prone northeastern region of Kenya, whereas Ae. ochraceus is a homogeneous population that appears to be undergoing expansion. Characterization of specimens from a RVF-prone site in Senegal, where Ae. ochraceus is a primary vector, revealed direct genetic links between the two Ae. ochraceus populations from both countries. Our data strongly suggest that unlike Ae. mcintoshi, Ae. ochraceus appears to be a relatively recent, single 'introduction' into Kenya. These results, together with increasing isolations from this vector, indicate that Ae. ochraceus will likely be of greater epidemiological importance in future RVF outbreaks in Kenya. Furthermore, the overall vector complexity calls into question the feasibility of mosquito population control approaches reliant on genetic modification.Author Summary: Despite the threat posed by Rift Valley fever (RVF), poor understanding of the disease epidemiology exists with respect to vector population structure in relation to differential outbreak patterns and future vector genetic control. Here, nuclear and mtDNA data reveal genetic complexities of RVF key vectors (Aedes mcintoshi and Ae. ochraceus) partly explaining the disease outbreak pattern in Kenya. While anticipating population differentiation, we found that the hitherto known Ae. mcintoshi in fact comprises a species complex, with one unique species restricted to northeastern Kenya where outbreaks have increased in frequency with evidence for new involvement of Ae. ochraceus in RVF epidemiology. We infer a relatively recent, single “introduction” of Ae. ochraceus into Kenya with genetic links to a RVF hotspot in Senegal. Ultimately, our findings provide an understanding of how the two primary mosquito vector species impact RVF, which is critical to the potential prediction of the emergence and spread of the disease in Kenya.