Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus. Foot-and-mouth disease virus strain:Serotype O | isolate:O1BFS 1860

Sequence diversity of foot-and-mouth disease (FMD) virus populations within a host reflect events that drive the fine-scale evolution of the virus. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. Data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks.