Location: Genomics and Bioinformatics Research
Project Number: 6066-21310-006-022-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2022
End Date: Aug 31, 2025
Objective:
1. To develop a prototype metagenomic xenosurveillance program.
2. To monitor wet markets at several sites in southwestern Nigeria by trapping flies that come into physical contact with meat products and animals that are processed and sold in these markets.
Approach:
The sub-awardee of the cooperator in Ede, Nigeria will collect and sequence metagenomes from pools of arthropods trapped at selected markets over time. ARS will work with the cooperator to develop and refine the metagenomics analysis workflows and joint teams will use high performance computers to process data to identify known human, animal, and zoonotic pathogens as well as assemble and analyze metagenomes for new, emerging pathogens as well. These data will be used for rapid phylodynamic modeling of detected pathogens to ascertain spatio-temporal transmission dynamics and population risk. Together these approaches allow for targeted prevention and control in low-resource settings and provide much-needed data on how to prevent animal disease before it reaches the US.
Musca domestica (the common housefly) feeds and breeds in fecal and decaying matter. As such, these filth flies often act as mechanical vectors or reservoirs of pathogens with and without direct ingestion of the pathogen. Houseflies are often found in and around areas of high economic and human importance: food distribution areas such as abattoirs, wet market trade hubs, and pastoral grounds. The cooperator and sub-awardee will collect ~5,000 houseflies at each of the five sites in Osun and Ondo states in Nigeria, including shops processing “wild game meat” (both in large and small markets), and small/large herd pastoral communities. Samples will be collected, processed, and sequenced locally in Ede. Collecting these flies will be of high value to the community, as removing these pests from the environment improves the perceived cleanliness of food production and distribution and reduces arthropod nuisance at the individual level. Expected outcome: RNA and DNA metagenomics of M. domestica (as well as other muscid spp.) across these sites will provide a cross-sectional prevalence snapshot of viral, bacterial, and parasitic pathogens of One Health concern. Secondary outcomes include insight into the basic ecology of these pests; and ecological diversity of muscid spp. (e.g., M. sorbens [eye fly] or blood-feeding stable flies such as Stomoxys calcitrans) collected at each site and their potential role as mechanical vectors and reservoirs. Where virus sequence assembly is possible, ARS and the cooperator will explore the reconstruction of recombinant versions of this virus using approaches established in the cooperator’s laboratory to further understand the biology of these pathogens in the laboratory (in vitro).
