Sequence of the S fragment of foot-and-mouth disease virus type A12

The foot-and-mouth disease virus (FMDV) genome contains a 5' untranslated region (S fragment) capable of forming a stem-loop structure of over 350 bases, which is separated from the remainder of the genome by a homopolymeric cytidylic acid tract (poly(C)) of variable length. The sequence of the S fragment of serotype A12 appears more similar to those of type O1 or type C3 than to subtype A10. The relatively large difference between the S fragment sequences of two type A viruses suggests that the sequences per se of this region of the genome are not critical for the maintenance of function, and suggests the possibility of a relatively recent recombination event within the poly(C) region of the A12 genome.