The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus

•45 full FMDV genomes were analysed from farms infected in the UK during 2007.•Analyses revealed intra-herd clustering consistent with virus transmission events.•Inter-herd sequence differences were estimated to be 4.6 nucleotides.•Random selection of 1 sequence from each herd generated similar transmission trees.•These results will help to design cost-effective approaches for the control of FMD.