Figure 2

Sequence changes within Gag epitopes restricted by HLA-B*14, B*27 and B*57 identified by ultra-deep sequencing of an HIV transmission pair aligned to CRF01_AE clade consensus (bold) and B clade consensus sequence (grey). The frequency of minor variant haplotypes at the HLA-B*57 Gag-ISW9, HLA-B*57 Gag-KF11, HLA-B*57 Gag-TW10, HLA-B*27 Gag-KK10, and HLA-B*14 Gag-DA9 epitopes above a cut-off of 1% are shown. Depth of coverage ranges from 560 to 240,000 reads. Position 146 (flanking HLA-B*57 Gag-ISW9), associated with selection of an HLA-B*57/58:01-selected A146P processing mutation in B clade infection, is also shown. Minor variant frequencies are rounded off to the nearest 1%.