Figure 2.

S-fragment sequences for QENP and uEA isolates can form single stem loops with similar secondary RNA structure as the S-fragments of other FMDV isolates. Separate multiple sequence alignments (MSAs) were prepared for sequences of Eurasian, SAT, QENP and uEA clusters using X-INS-i algorithm implemented in the MAFFT package. Secondary structure prediction was calculated using RNAalifold algorithm implemented in the ViennaRNA package and structures were visualized in the Forna visualization server. Sequencing of the FMDV genome often results in ambiguity at the beginning of the genome and at regions flanking the poly(C) region, therefore only regions of the S-fragment which showed unique base calling for the whole alignment were included in these RNA secondary structure predictions. Sequence at the apex of each conserved RNA secondary structure is shown, where pairing between two nucleotides is highlighted in red.