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

Date Published: December 4, 2014

Publisher: Public Library of Science

Author(s): David P. Tchouassi, Armanda D. S. Bastos, Catherine L. Sole, Mawlouth Diallo, Joel Lutomiah, James Mutisya, Francis Mulwa, Christian Borgemeister, Rosemary Sang, Baldwyn Torto, Matthew Kasper.

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.

Partial Text: Rift Valley fever (RVF) virus, a mosquito-borne Phlebovirus, occurs in endemic/epidemic proportions in Africa, causing mortality and morbidity in humans and livestock with severe public health and economic consequences [1], [2]. Following its initial detection in Kenya in 1912 [3], the virus has spread to several countries in Africa causing frequent and sporadic RVF outbreaks [4]–[6] and has expanded as far as the Arabian peninsula [7]. An analogous pattern is evident in Kenya where the disease has spread from its focal point in the Rift Valley province in 1931 to almost the entire country [5] with each subsequent outbreak covering a wider area of Kenya. Cumulatively, epizootics of the disease in affected parts of the world have resulted in the deaths of millions of domestic animals, and hundreds of thousands of human infections culminating in over 2000 deaths [5].

We first analyzed the genetic diversity of both species in Kenya. Our analyses revealed a high degree of diversity over the range sampled for both Ae. mcintoshi and Ae. ochraceus, characterized by high haplotype but low nucleotide diversities. Of the 165 samples examined for Ae. mcintoshi, we detected 136 haplotypes (haplotype diversity ± standard deviation, Hd = 0.997±0.002) but with low nucleotide diversity (Pi = 0.041±0.001) for the COI locus. An analogous pattern was evident for the ITS locus where 55 haplotypes were identified from the 79 samples examined (Hd = 0.883±0.020; Pi = 0.023±0.001). For populations of Ae. ochraceus, a total of 60 haplotypes were recovered from the 67 COI gene sequences generated, corresponding to a haplotype diversity (Hd) of 0.9964±0.003 and a nucleotide diversity (Pi) of 0.006±0.003; a pattern also mirrored for the ITS locus which yielded 32 haplotypes from the 32 samples examined (Hd = 0.998±0.003; Pi = 0.005±0.001). Regarding the COI locus as would be expected for a coding gene, the proportion of base position mutations for Ae. mcintoshi was 3rd>1st>2nd, with 205 (85%) of the mutations occurring in the 3rd base position, 33 (14%) in the 1st base position and the remaining 3 (1%) being attributed to 2nd base position mutations. A similar pattern was evident for Ae. ochraceus with mutations occurring at 14 (13%) 1st base positions, 2 (2%) 2nd base positions, with the remaining 91 (85%) occurring at the 3rd base position. There was a high frequency of single haplotypes with just a few of these being shared by geographically diverse localities (Figures S1 and S2). The haplotypes generated in this study have been deposited in GenBank under accession numbers KJ940551–KJ940692 (Ae. mcintoshi from Kenya, COI gene sequences); KJ940693–KJ940754 (Ae. ochraceus from Kenya, COI gene sequences); KJ940755–KJ940765 (Aedes from Senegal, COI gene sequences); KJ940766–KJ940823 (Ae. mcintoshi from Kenya, ITS sequences); KJ940824–KJ940832 (Aedes from Senegal, ITS sequences); KJ940833–KJ940866 (Ae. ochraceus from Kenya, ITS sequences).

We present the first study using DNA-based markers to assess the level of genetic diversity, distribution and demographic patterns of Ae. mcintoshi and Ae. ochraceus, and how they relate to differential patterns of RVF occurrence in Kenya. Based on the markers used, our data suggest that what is called Ae. mcintoshi consists of at least four distinct clades which were well supported by ML and BI analyses; Ae. ochraceus, clustered within two clades comprising a uniform homogeneous population for samples in Kenya but with substructure with respect to some of the samples from Senegal. Phylogenetic evidence for Ae. mcintoshi from COI and ITS individual datasets is slightly disconcordant, although patterns are more pronounced with concatenated (COI+ITS) data. A possible explanation for the observed incongruence in the phylogenies of the individual genes could be due to the varying sample sizes for the individual datasets. The concatenated data may therefore provide a clearer pattern because combining data from multiple genes can overcome misleading signal in individual genes [60], [61]. Taken together, our results provide strong evidence for genetic structure in Ae. mcintoshi from Kenya and Senegal.



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