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Research Project: Molecular Characterization and Epidemiological Surveillance of Arboviruses in Kenya’s Wildlife

Location: Foreign Arthropod Borne Animal Disease Research

Project Number: 3022-32000-024-007-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2021
End Date: Aug 31, 2023

The objective of this agreement is to develop and apply new technology to detect and characterize arboviruses present in Kenyan wildlife that could pose emerging animal disease threats and develop a baseline of virus population variability. Study areas will be selected to inform predictive models regarding climate change and wildlife-livestock interaction on arbovirus emergence and diversity.

At least three targeted collection sites will be selected to represent different geographical areas including area near a livestock/wildlife interface. This will assess geographical variation and impact of livestock encroachment into wild areas. Also sampling these habitats over time will allow for modeling of how virus circulation (host-vector-virus) interactions will change in a changing climate. Sera and blood samples from wildlife will be assayed by different techniques. The cooperative team will develop a panel of family specific RT-qPCR assays for alphaviruses, bunyaviruses, flaviviruses, orbiviruses and rhabdoviruses. Multiplex assays will be developed where scientifically reasonable and technically possible. The initial development and validation will be done using standard laboratory real-time thermocyclers. Once developed the assay will be adapted and equivalency validated on the field-based system (eg. BioMeme). Positive samples will be subjected to further characterization by next generation sequencing technology. Briefly, a virus capture isolation procedure will be developed to enhance the viral target RNA in the sample. Unbiased metagenomic sequencing will be used to generate sequence data using the Minion platforms. If the unbiased approach does not produce sufficient viral sequence reads, then family specific targeted sequencing approaches will be developed. The data generated in this project will be used to provide baseline arbovirus prevalence that could emerge and threaten animal and public health. In addition, the virus population variability will be used to inform risk models in future studies.