SIVmac251 gag from challenge aliquot
SIVmac251 RNA was extracted from challenge aliquot. 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).