HOXD13 and scarlet fever: To investigate the impact of the 27 M1UK lineage-defining SNPs and 4 deletions on global gene transcription, we performed complete genome sequencing and RNA-seq analysis of three Australian M1UK genotype S. pyogenes isolates; SP1380 (scarlet fever; ssa+, speC+, spd1+, speA+), SP1384 (scarlet fever; ssa−, speC−, spd1−, speA+), and SP1448 (invasive disease; ssa−, speC−, spd1−, speA+) (Fig. 1b and Supplementary Fig. 2).