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ARS Home » Research » Research Project #440427

Research Project: Detection and Characterization of Potential Emerging Arboviruses in Brazil

Location: Foreign Arthropod Borne Animal Disease Research

Project Number: 3022-32000-025-005-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2021
End Date: Jul 31, 2024

The objective of this agreement is to develop and/or apply new ARS technology to detect and characterize arboviruses present in Brazil that could pose emerging animal disease threats and develop a baseline of virus population variability. The area to be investigated will include boundary areas between rural and sylvatic habitats that will inform predictive models of effects of climate change, deforestation and livestock encroachment into wild areas effects on potent emergence of arboviruses.

At least three targeted mosquito collection sites will be selected to represent different geographical areas including the Amazon for mosquito collections. The areas where mosquitoes will be sampled will be on the boundary between rural and sylvatic habitats. This will assess the impact of deforestation or animal livestock encroachment into wild areas impact on enzootic virus transmission due to potential increased contact with wild animals. Also sampling these habitats 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. Where scientifically reasonable and technically possible multiplex assays will be developed. 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, Illumina Miseq and NextSeq200 platforms. In the event that 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 threat animal and public health. In addition, the virus population variability will be used to inform risk models in future studies.