SIVmac251 gag from nave macaque
SIVmac251 RNA was extracted around peak viraemia (between day 7 and 21).  Full length SIV gag was amplified as a single amplicon using forward (CCTGAGTACGGCTGAGTGAA) and reverse (TGGACCTAACTCTATTCCTGTTACA) primers.  Bar-coded libraries of amplicons were made using Nextera XT library preparation kit, equimolar amounts of each sample sequenced in 250 bp paired-end MiSeq V500 sequencing reactions (both Illumina).