Primers used to determine the relative fitness of FMDV populations.

aViral populations which are specifically discriminated by the primer indicated in b.
bNucleotide sequence of the primers used. Letters in bold are nucleotides that have been modified with respect to the genomic sequence of the FMDV C-S8c1, and that serve to discriminate among different populations.
cGenomic orientation of primer: forward (F) or reverse (R).
dHybridization temperature used in the real time RT-PCR assays to discriminate the competing RNAs. “--” indicates that this primer does not discriminate specifically among mutant genomes.
ePosition of the 5′-nucleotide of the primer; numbering is that described in [93].
fComplementary primer used in each case during RT-PCR amplification. “--” indicates that this primer does not discriminate specifically among any mutant genomes and is used as the complementary for the RT-PCR reaction.