Full genome sequencing to identify determinants that impact upon foot-and- mouth disease virus strains with a potential for enhanced transmission in endemic settings in Africa (360G-Wellcome-104017_Z_14_Z)

This proposal aims to investigate the evolutionary characteristics of FMDV field strains in endemic settings of Africa that could be associated with future epidemics/spread. The main focus is to understand the molecular basis and factors associated with overt antigenicity and/or transmission ability of FMDV in different geographic areas within endemic settings. The unique significance of project will be identification of early genomic changes that are likely to lead to broader antigenic and virulence, the knowledge of which could be crucial in defining early interventions, including vaccine strain selection before such changes result in wide-scale epidemics of FMD. In this study, molecular epidemiology and virus evolution data will be generated from persistently and/or naturally infected animals (cattle and buffalos) and following FMD outbreaks in specified geographic locations, whereas pathogenicity and transmission dynamics will be assessed through targeted experimental infections of animals. This study will also generate whole genome sequence data of the circulating FMD viruses and unravel viral genotypes and/or phenotypes in specific geographic areas, the information that could be linked with persistence, pathogenicity and phylogeography of the field strains. The in-depth genetic analysis of sequences will further unravel the molecular determinants of FMDV endemicity in specific geographic locations in Africa. This information, together with antigenicity data, could be used for recommendation of appropriate vaccines to use in specific geographic areas with overt FMD outbreaks.