File:Ppat.1000050.g002.tif

English: Analysis of sequence data. A) Statistical parsimony analysis by TCS [19] of complete genome sequences of 14 foot-and-mouth disease viruses (FMDV); connecting lines represent a nucleotide substitution, thicker lines represent non-synonymous substitutions, with substitutions indicative of adaptation to cell culture coloured green. Sequenced haplotypes (red circles), and putative ancestral virus haplotypes (white circles) are shown. AY593815 is a previously published sequence [21] of FMDV O1 BFS 1860. The asterisk indicates the start of the tree in 2B). B) Lesion age derived infection profiles of holdings overlaid with the outbreak virus geneology. The orange shading estimates the time when animals with lesions were present from the oldest lesion age at post-mortem [22]. For IP2c, there were no clinical signs of disease. The light blue shading represents incubation periods for each holding, estimated to begin no more than 14 days prior to appearance of lesions [23]. The dark blue shading is the infection date based on the most likely incubation time for this strain of 2–5 days [24]. Each UK 2007 outbreak virus haplotype is plotted according to the time the sample was taken from the affected animal (x axis). The dashed lines link the TCS tree together but do not denote any genetic change.