Fig. 1

Plasma HIV RNA viral load and CD4+ T cell counts for HLA-B*27:05/57:01+ subject R097 and his transmission partner R096 and phylogenetic analysis of HIV sequences showing epidemiological linkage and sequence diversity in transmission pair R096/R097. a Transmission pair donor, R096. b Transmission pair recipient, R097. ‘Early’ and ‘late’ time points of sampling for sequencing are shown (see c). ‘Time 0’ represents the time of diagnosis of recipient R097. The horizontal dotted line represents the limit of detection (LOD) of the viral load assay (40 HIV RNA copies/ml). Grey shading indicates the period during which the subject received antiretroviral (ART) therapy. c Maximum likelihood phylogenetic tree of 1091 bp alignment of RNA (ultra-deep consensus) sequences across the Gag p17 and p24 genes. The donor R096 sequence is shown in blue. Early and late sequencing time points are shown in a. The early R097 sequences are shown in red (n = 2). The late (post-2 year) sequences for R097 are shown in green (n = 11). The early and late sequences form two distinct clusters indicating considerable intra-host sequence diversification over time. 143 B clade reference sequences from the US and UK collected between 2003 and 2011 from the Los Alamos database (http://www.hiv.lanl.gov/) are shown in black. Bootstrap values for the R097 sequence clusters based on 1000 bootstrap replicates are shown in italics