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

Location: Foreign Arthropod Borne Animal Disease Research

Project Number: 3022-32000-024-004-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2021
End Date: Aug 31, 2025

The objective of this agreement is to develop reagent and new technology for detection and surveillance of arboviruses that could pose emerging animal disease threats and develop a baseline of virus population variability. The area to be investigated will be selected to inform predictive models regarding climate change and encroachment of livestock into wild areas effect on arbovirus emergence.

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 animal 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. Mosquitoes will be sorted by species and deployable point-of-need tools will be developed to quickly identify and characterize viruses. 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. For example: a mosquito-borne assay might include only the first three virus families. 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 generated 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 initial study was conducted with commercial software (such as CLC Genomics Workbench, Genetic). The data will also be subjected to more sophisticated computational virus population genetic analysis that is being developed in another project. 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.