Substitutions found in FMDV mutants that encode one VPg, upon passage in BHK–21 cells ^a.

a<p>The consensus sequence of the entire viral genome was determined for FMDV populations V3, V19–4 and V15–9 (series A and B) after 2 passages in cell culture (experiment described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010735#pone-0010735-g003" target="_blank">Figure 3</a>). The sequence of viral genomic regions 2C, 3A, 3B (VPg), 3C and 3D (residues from genomic position 4200 to 8115) was determined for 5 independent biological clones isolated from population V3A at passage 1. The origin of each population is described in the text and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010735#pone-0010735-g003" target="_blank">Figure 3</a>.</p>b<p>FMDV genomic region analysed <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010735#pone.0010735-Ryan1" target="_blank">[15]</a>.</p>c<p>Mutations and deduced amino acid substitutions are relative to the sequence of the parental clone FMDV WT (pMT28, described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010735#s4" target="_blank">Materials and Methods</a>); residue numbering is according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010735#pone.0010735-Baranowski1" target="_blank">[49]</a>. Amino acid residues (single–letter code) are numbered individually for each protein from the N– to the C–terminus. Procedures for nucleotide sequencing and identification of FMDV genomic regions are described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010735#s4" target="_blank">Materials and Methods</a>.</p>d<p>Populations and biological clones in which the substitutions indicated in ^c were found.</p>e<p>Mutation C4507U (that corresponds to amino acid substitution R55W in 2C) was repeatedly found in 3 out of 6 mutant FMDV populations at passage 2, and 2 out of 5 biological clones from population V3A at passage 1 (underlined).