Epidemiology of Foot and Mouth Disease Virus in Uganda

Abstract

The continued endemicity of foot and mouth disease virus (FMDV) in East Africa has significant implications for livestock production and poverty reduction, yet its complex epidemiology in this region remains poorly understood. Here we describe a series of studies aimed at elucidating the epidemiology of FMDV in Ugandan cattle. Specifically, our goals were to identify heterogeneities in risk of FMDV exposure and describe the characteristics of high-risk areas, including sources of FMDV dissemination. In Chapter 1, we describe the current FMDV situation in Uganda. In Chapter 2, we integrate country-wide serology and questionnaire data to identify FMDV spatial clusters and their associated risk factors. In Chapter 3, we use FMDV genomic data from across East Africa to describe transmission statistics and identify the characteristics of areas in which FMDV tends to remain circulating. In Chapter 4, we develop novel regression tools to analyze georeferenced phylogenies. These novel tools allow one to identify the direction of viral spread, thus pinpointing areas from which FMDV tends to disseminate. Using serology data (Chapter 2), spatial clustering of the disease was evident, with highest risk demonstrated near international borders. Additionally, high cattle density, low annual rainfall, and pastoralism were associated with increased likelihood of FMD seropositivity. In Chapter 3, we identified statistical evidence of long-distance transmission events, and that FMDV tends to remain circulating in areas of high cattle density, high human population density, and near livestock markets. In Chapter 4, we developed novel regression tools to describe areas in which FMDV tends to remain circulating and areas from which FMDV tends to disperse (viral sources). We identified areas near livestock markets and areas with high cattle densities as sources of serotype O. Collectively, these results provide insights into the complex epidemiology of FMDV in Uganda and will help inform control strategies in Uganda and other FMDV-endemic settings. Supplemental files, published separately, contain two files referenced in Chapter 3: 1. Supplemental File A: Initial phylogenetic tree constructed for selection of a monophyletic clade containing sequences recently circulating in East Africa. 2. Supplemental File B: Sampling data for FMDV sequences used in the BEAST and seraphim analyses.