As present in the intra-host population at 52 months post diagnosis (Figure
As present in the intra-host population at 52 months post diagnosis (Figure 6b, Additional file 1: Figure S1). This demonstrated diversity at only 2.6 of all amino acid residues, of which the majority (1.1 ) were in Env, a highly variable region of the genome where Necrosulfonamide supplier mutations are driven largely by neutralizing antibody responses. Of the remaining sites of diversity, 16 were within or flanking recognized HLA-B*27/-B*57 epitopes. In both the donor/recipientBrener et al. Retrovirology (2015) 12:Page 8 ofFigure 7 Schematic representation of sites of complete amino acid mismatch between the donor and recipient full-length HIV sequences. The recipient consensus sequence at 52 months is aligned to the donor consensus sequence at 8 months (the latter being the closest representation of the transmitted HIV sequence). The sites shown in this figure are complete mismatches between donor and recipient identified in the heat map PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26795252 analysis (red squares, Figure 6a) The mismatched residue is indicated in bold. HLA-B*27:05, B*57:01 and C*01:02-restricted epitopes are shown in red, blue and green respectively. Mismatched residues that do not fall within a relevant HLA-Class I epitope are shown in yellow.comparison (Figure 6a) and intra-host diversity plot (Figure 6b) the evolving sites in Gag were frequently within known or predicted CTL epitopes restricted by the recipient’s HLA alleles, whereas those outside of Gag, especially in Env or Nef, were PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27484364 rarely within known or predicted epitopes (Figure 6c, d).Sequence changes in the donor reflect escape polymorphisms selected in known epitopesFinally, we examined the sequences in the donor, who progressed despite possessing the protective HLAA*32:01, HLA-B*13:02 and HLA-B*14:01 alleles. Compared to the full-length CRF01_AE clade consensus sequence, there are six epitopes at which HLA-associated mutations are present in the donor, two of which are in p24 Gag. These are within epitopes restricted by HLAB*13:02 (Gag 135?43, `VV9′) and B*14:01 (Gag 298?306, `DA9′) respectively (Additional file 2: Figure S2). Thus, as in the recipient, progression to HIV disease in the donor was associated with mutations in critical p24 Gag epitopes.Discussion This study capitalizes on longitudinal data from a wellcharacterized transmission pair, for whom we wereable to maximize the depth (ultra-deep approach) and breadth (full-length HIV genomes) of sequence resolution. This allowed us to quantify precisely the evolution of escape mutations, including minor variants, in the context of what would usually be regarded as a highly favorable combination of HLA alleles, HLA-B*27:05 and HLA-B*57:01. Since both these alleles occur at a very low frequency within the Thai population (approximately 0.2 and 1.4 respectively [34]) finding this haplotype in the context of CRF01_AE clade infection is an `accident of nature’ which provides a unique opportunity to study the mechanisms of immune control. There are conflicting data regarding the extent to which HLA-B*57 may be protective in Thai cohorts. Although a recent study in a particular Thai cohort, where the median CD4+ T cell count was only 86 T cells/ mm3, reported that HLA-B*57:01 was protective [34], a parallel study of 116 transmission pairs found no benefit of HLA-B*57 [35]. The latter result fits with the picture we describe in our HLA-B*57-positive recipient, and is consistent with the abrogation of HLA-B*57-restricted Gag epitopes due to pre-existing polymorphisms in CRF01_AE.
