Location: Foreign Animal Disease Research
Project Number: 3022-32000-064-054-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 3, 2026
End Date: Jul 30, 2027
Objective:
The research project aims to generate and analyze viral genomic data from aphthoviruses detected in free-ranging deer populations in the United States (U.S.) to improve understanding of viral evolution, transmission continuity, and spatial spread patterns relevant to foot-and-mouth disease virus (FMDV) preparedness. The primary goal is to determine whether aphthoviruses circulating in wildlife populations exhibit genetic signatures consistent with sustained transmission, lineage turnover, or repeated introductions. This work will strengthen national preparedness for foreign animal disease (FAD) incursions by providing genomic evidence necessary to resolve transmission histories, characterize viral diversity, and inform epidemiological modeling and surveillance strategies associated with wildlife–livestock interface risks.
Approach:
In collaboration with the Agricultural Research Service (ARS) and project partners, the cooperator will conduct genomic sequencing and evolutionary analyses of aphthoviruses detected in U.S. deer populations. The approach includes:
1. Sample Processing and Viral Detection: The cooperator will receive and process biological samples collected from free-ranging deer, including nasal swabs, serum, or archived specimens. Laboratory workflows will include viral metagenomic screening, nucleic acid extraction, and quality-assurance procedures to detect and characterize aphthoviruses in wildlife samples.
2. Genomic Sequencing and Assembly: The cooperator will perform high-throughput sequencing of aphthovirus-positive samples and generate high-quality viral genome assemblies. Sequencing protocols will be optimized to recover complete or near-complete viral genomes suitable for downstream phylogenetic and evolutionary analyses.
3. Phylogenetic and Evolutionary Analysis: Viral genome sequences will be analyzed to reconstruct evolutionary relationships among aphthovirus lineages circulating in deer populations. Analyses will quantify lineage diversity, genetic continuity, and rates of evolutionary change to evaluate evidence for persistent viral circulation versus episodic introduction events.
4. Phylogeographic and Transmission Structure Inference: The cooperator will integrate viral sequence data with spatial and temporal metadata to infer patterns of viral movement, geographic clustering, and transmission connectivity among wildlife populations. These analyses will evaluate whether viral spread reflects localized circulation, regional transmission corridors, or repeated reintroduction events.
5. Data Integration and Dissemination: Genomic datasets, analytical outputs, and associated metadata will be curated and shared with ARS and collaborating research teams to support downstream spatial epidemiological modeling and risk assessments. Research findings will be disseminated through peer-reviewed publications, scientific presentations, and technical reports.
6. A postdoctoral researcher or equivalent scientific personnel, supervised by the cooperator, will conduct sequencing, genomic analyses, and data interpretation to ensure rigorous scientific implementation.