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Research Project: Foot-and-Mouth Disease Virus Surveillance in Kenyan Livestock by Sampling at Animal Concentration Points

Location: Foreign Animal Disease Research

Project Number: 3022-32000-064-021-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Jul 1, 2021
End Date: Jun 30, 2025

The purpose of this project is to evaluate sampling of subclinical animals at livestock markets and slaughter points as a strategy for genomic surveillance of Foot-and-Mouth Disease Virus (FMDV) under endemic conditions in Kenya. Livestock markets and slaughterhouses function as concentration points where animals and humans from distant and distinct sources commingle and potentially exchange pathogens like FMDV. This project extends research conducted over the past several years in Kenya by our international team of scientists from ARS, PIADC and the collaborators from Kenya FMD-Lab, Kenya Wildlife Service, and University of Minnesota. Previously, sub-clinical FMDVs circulating in the Masai Mara ecosystem in southern Kenya through longitudinal sampling of herds were characterized, including identifying circulating FMDV strains and determining the incidence of subclinical and clinical infection. ARS will now investigate the extent to which viruses recovered at concentration points reflect the prevalence and diversity found in the source populations, which have been inferred through serial cross-sectional sampling of farms and determine whether they can serve as sentinels for the early detection of outbreak strains identified through the current status quo based on passive outbreak surveillance. Specific activities will include: 1. Establish a surveillance system to obtain cattle, goat, and sheep samples and associated epidemiological data (including origin and destination) from livestock markets and slaughter points. 2. Determine the prevalence and strains of FMDV circulating as clinical and sub-clinical infections in Kenya. 3. Quantify the proportion of infected cattle, goats, and sheep passing through livestock markets during and between outbreaks. 4. Genetically and antigenically characterize FMDV strains and determine their relationship to vaccine strains.

1. A sample protocol will be developed and deployed at 4 markets in the pastoral study area in the Masai Mara ecosystem and 2 terminal slaughterhouses near Nairobi. Market concentration points will be selected from areas in which historical samples are available from previous projects, as well as to target areas with frequent transboundary movements from Tanzania or transhumance migratory herd movements. These markets are considered “tertiary” markets and represent the starting point of supply chains. Concentration points will be sampled routinely during the absence of clinical outbreaks, and with higher frequency during clinical outbreaks reported in the area. 2. Serological and oropharyngeal fluid sampling will be conducted at concentration points to quantify the proportion of infected cattle, goats, and sheep. Among other epidemiological data, data on an animal’s origin and destination will be used to characterize circulating viruses in the source population as well as to characterize the risk of long-distance transport of virus. 3. To determine whether viruses recovered from markets reflect the diversity and prevalence of FMDVs in the source population, and whether they can serve as sentinels for the early detection of emerging outbreak strains, we will conduct farm-based cross-sectional sampling of herds within the primary study area. Additionally, clinical samples will be purposively collected from outbreaks reported in the study area and from other regions of Kenya. 4. A long-term system for outbreak reporting, sample collection, and stakeholder engagement in the study area to support project activities will be established through funding, training, and equipping community animal health liaisons. 5. Samples will be tested by antigen ELISA and serological ELISA to detect structural and non-structural FMDV protein antibodies. Field samples from acute and subclinical infections will be sent to AR, PIADC for real-time RT-PCR, virus isolation and strain characterization by sequence acquisition and analysis. Spatial epidemiological and phylogenetic analysis will be performed by collaborators from the University of Minnesota.