Figure 6

Comparison of inter- and intra-host diversity of HIV quasispecies in a transmission pair. a Heat map representation of inter-host amino acid diversity across the full-length HIV genome, comparing donor and recipient. For the baseline, we used the donor sequence at 8 months post-diagnosis (which in this case represents the closest approximation of the founder virus); variation in the recipient at 52 months post-diagnosis is compared to this baseline. Each square represents a single codon, coloured to reflect the percentage of sequences in the recipient that differ from the consensus residue in the donor. b Heat map representation of intra-host amino acid diversity in the recipient at 52 months post-diagnosis. For the baseline, we used the recipient consensus sequence at 52 months post-diagnosis to which the intra-host recipient population at the same timepoint is compared. Each square represents a single codon coloured to reflect the percentage of minor variants in the recipient that differ from the consensus (‘baseline’) residue. c Percentage of true amino acid mismatches (excluding positions where the recipient’s sequence was represented as a minor variant in the donor) between donor and recipient sequences by gene. The proportion of mismatches at sites where there is a known or predicted association with the recipient’s HLA alleles is indicated. d Percentage of diverse amino acid sites (variability >10%) in the recipient intra-host population by gene. The proportion of diverse sites where there is a known or predicted association with the recipient’s HLA alleles is indicated.