Population genetics of two key mosquito vectors of Rift Valley Fever virus reveals new insights into the changing disease outbreak patterns in Kenya

Abstract

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.

Figure 1. Map of Kenya showing location of study sites and geographical distribution of putative species within what is called Ae. mcintoshi in Kenya, delineated on the basis of the COI barcoding region.

The broad sampling areas are color-coded as follows: red (clade II; green (clade I); blue (clade IV).

Figure 2. Maximum likelihood tree derived for concatenated dataset (COI+ITS) of A). Ae. mcintoshi and B) Ae. ochraceus, from Kenya and Senegal.

Bootstrap values and Bayesian support values are shown above and below relevant nodes, respectively. Sequence of Ae. ochraceus indicated as outgroup for Ae. mcintoshi and vice versa. Taxon abbreviations follow those provided in Table 2 with numbers corresponding to specific sequence samples.

Figure 3. Chronogram of divergence times for Ae. mcintoshi and Ae. ochraceus from Kenya and Senegal represented on a maximum likelihood tree obtained from the analysis of the mtDNA dataset.

Node positions indicate mean estimated divergence times and numbers on nodes the BS values. Taxon abbreviations follow those provided in Table 2 with arbitrary numbers indicating specific sequence samples.