Location: Zoonotic and Emerging Disease Research
Project Number: 3022-32000-021-031-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 1, 2026
End Date: Jul 31, 2028
Objective:
The objective of this project is to strengthen early detection of emerging and high-consequence zoonotic pathogens in Nigeria including henipaviruses and crimean congo hemoragic fever (CCHF) to better understand threats that could affect U.S. agriculture, livestock health, food security, and public health preparedness. Nigeria is an important sentinel location because it has high biodiversity, diverse bat populations (including those known to carry henipaviruses), expanding agricultural interfaces, active wildlife trade and hunting, mixed-species farming systems, tick s known to carry CCHF. These conditions create opportunities for pathogens to circulate silently in wildlife, ticks, small mammals, and domestic animals before they are recognized as broader agricultural or public health threats. Objective 1: Detect emerging viral threats in wildlife and agricultural interfaces. The project will use metatranscriptomic sequencing of bat samples to characterize viral diversity in Nigerian bat populations and identify henipa and closely related viruses with potential relevance to animal health, zoonotic spillover, and agricultural preparedness. Particular attention will be given to henipaviruses and other viruses that may signal emerging risk to livestock, companion animals, or people working at animal interfaces.
Objective 2: Evaluate CCHF virus exposure and circulation in mixed agricultural systems. The project will assess evidence of CCHFV exposure and infection in ticks, small mammals, pigs, and other livestock in agricultural and peri-domestic settings. This will help determine whether CCHFV is circulating undetected in mixed farming systems and whether pigs, small mammals, or tick-host interactions may contribute to virus maintenance or exposure risk. Objective 3: Integrate genomic, serologic, ecological, and farm-interface data to identify risk patterns. Sequencing, serology, tick data, and available field metadata will be analyzed together to identify host species, locations, farming practices, and ecological interfaces associated with increased pathogen detection or exposure. This integrated approach will help define how wildlife contact, mixed farming, animal movement, and vector presence may shape pathogen emergence and persistence.
Approach:
IGH and USDA-ARS will implement a focused One Health detection project using existing field partnerships, sample collections, sequencing capacity, and bioinformatics infrastructure in Nigeria. Bat oral and rectal swabs, blood or plasma, and available archived specimens will be prioritized for viral metatranscriptomics to define the diversity of henipaviruses and RNA viruses present in bat populations from selected regions. Viral sequences will be classified, assembled when possible, and compared with global datasets to assess relatedness to known animal or zoonotic pathogens. In parallel, the project will evaluate CCHFV risk in agricultural and peri-domestic settings, especially in areas with mixed farming practices and overlap among livestock, pigs, small mammals, ticks, and wildlife. Serum or plasma samples will be tested using available CCHFV serologic assays to identify evidence of prior exposure. Swabs, tissues, and ticks may be tested by molecular methods or sequenced when resources and sample quality permit. Opportunistically collected ticks will be identified and archived or tested to determine whether CCHFV-associated tick species are present in these production systems. Data will be analyzed by host species, geography, ecological setting, and production practice to identify preliminary risk patterns. Metadata will be collected including location as well as information on location (ie market, farm, farming practices in use). The project will generate sequence data, serologic evidence, and field-based observations that can inform diagnostic development, risk modeling, and detection priorities.
This work is directly relevant to U.S. agriculture because emerging pathogens that threaten livestock and rural communities often arise first in regions where wildlife, vectors, and domestic animals interact intensively. Studying Nigeria provides an opportunity to identify viruses, host associations, and farming practices that may signal future risk before similar threats affect U.S. livestock systems. The findings will help USDA improve early detection, diagnostic readiness, and preparedness for high-consequence zoonotic and tick-borne pathogens that could affect animal agriculture, trade, and food security. The project being proposed is a multi year project. To mitigate risk only the first year of funding is being included. Based on the success of the project and the data generated addtional funds will be added.