Spatial and temporal distribution of Aedes mosquitoes, Dengue and Chikungunya Viruses and their Phylogeny along the Coastline of Kenya

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Ngala, Chome Jonathan
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Kenyatta University
There are arthropod-borne disease outbreaks as a result of pathogen influx including arboviruses which are transmitted by strains of Aedes species that occur periodically in varying spots in Kenya. However, there has been paucity of documented information on the epidemiology of Aedes mosquitoes involved in transmission of different strains of viruses. This cross sectional study determined spatial and temporal distribution of Aedes mosquitoes, Dengue and Chikungunya viruses, and their phylogeny and vector-virus co-infections during dry and wet seasons. Indoor and outdoor sampling of adults Aedes mosquitoes was done using Biogent Sentinel trap baited with solid carbon dioxide and Prokopack aspiration technique. Aedes mosquitoes were identified and sorted according to collection site, sex, physiological status and species using their morphological features and molecular techniques. Sentinel sites coordinates were recorded by Global Positioning System receiver with spatial and temporal maps generated using ArcGeographical information system. RNA was extracted from Aedes mosquitoes using Trizol®. Identification of Aedes species, Dengue and Chikungunya was done using Polymerase Chain Reaction. Sequencing of amplicons was done using Sanger high-throughput technique and their proportions analysed by R-statistics. Phylogeny tree files were generated using Randomised Accelerated Maximum Likelihood and trees plotted using interactive tree of life. A total of 37,220 Aedes mosquitoes belonging to eight species were collected and grouped in pools of 20 mosquitoes. Aedes aegypti formosus was dominant at 62.5%. Aedes aegypti aegypti was identified for the first time along the Coastline of Kenya. There was no effect of season on the distribution and proportion of Aedes species along the Coastline. Aedes mosquitoes belonged to the upper clade of the phylogenetic tree. Four serotypes of Dengue virus were identified with DENV-4 identified for the first time in Aedes mosquitoes in the region. Only the East/Central/South African (ECSA) genotype of Chikungunya virus was isolated and seasons did not influence the distribution of both viruses along the Coastline (p>0.001). Aedes mosquitoes were closely related to previous isolates and to those from Uganda, Senegal and Thailand. DENV-1 isolates were closely related to those from India, DENV-2 isolates were closely related to those from Pakistan, and DENV-3 isolates were closely related to those from Brazil while DENV-4 isolates were closely related to those from Haiti. Chikungunya ECSA genotype isolates were closely related to previous Kenyan isolates and to those from South Africa and Tanzania. There were co-infections of Dengue and Chikungunya viruses in Aedes mosquitoes. Aedes aegypti s.l and Aedes pembaensis had co-infections of all viruses. Prevalence of Dengue virus was at 7.9% while Chikungunya was at 2.1%. These results are important as they give information on areas of high risk for the virus outbreaks. Surveillance of entomological infection by viruses and implementation of their appropriate control measures should be taken by the Ministry of Health.
A Research Thesis submitted in Partial Fulfilment for the Award of the Degree of Doctor of Philosophy in Infectious diseases (Medical Parasitology) in the School of Medicine, Kenyatta University
Spatial, Temporal distribution, Aedes mosquitoes, Dengue, Chikungunya Viruses, Phylogeny, Coastline, Kenya