The estimated node effect plotted onto the phylogeny.

<p>The estimated phylogenetic effect of each node on log₁₀ viral load plotted back onto the phylogeny from the 652-sample BEAST analysis. The axis shows the time in years from the most recent sequence, which was taken in 2009. Branches have been colored by the scale of the effect. Clusters of branches have been collapsed to improve readability, and are colored by the average tip effect within each cluster. As the number of bifurcations in the tree reduces at around 17.5 years before 2009, this used as the threshold for collapsing. Nodes that have a similar effect on viral load cluster together, as expected if some of the variation in viral load is heritable.</p

Estimates of viral genetic influence on set-point viral load in HIV subtype B in the UK.

<p>Estimates of viral genetic influence on set-point viral load in HIV subtype B in the UK.</p

Change in viral load over time due to selection.

<p>The estimated log₁₀ change in viral load per year due to selection and environmental effects (see also <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004112#ppat.1004112.s002" target="_blank">Fig. S2</a>).</p

Confirmed structure of the complex recombinant.

<p>The confirmed structure of the complex A1/B/D/U recombinant specimen 34567 following maximum likelihood analysis with the CRF50_A1D specimens. CRF50_A1D regions are shown in green and subtype B regions are shown in blue.</p

Bootscanning plots for five A1/D recombinants.

<p>Bootscanning plots from Simplot sliding window analysis using a window size of 400(not HXB2 numbering). Subtype A is represented in red, subtype D in lavender, and subtype F (outgroup) in grey. All five specimens (33365, 8179, 40534, 11762, 12792) showed identical bootscanning plots, with five subtype A1 regions and four subtype D regions. A) Specimen 33365; b) Specimen 8179; c) Specimen 40534; d) Specimen 11762; e) Specimen 12792.</p

Emergence of CRF50_A1D.

<p>Time-scaled analysis of CRF50_A1D <i>pol</i> gene sequences using BEAST. Green sequences indicate the closest NCBI BLAST matches to the CRF50 sequences (all subtype A1); red sequences indicate A1 reference sequences; purple sequences indicate subtype D reference sequences. Outgroup subtype C sequences are shown in blue. Node values indicate the posterior probability of each node. The five full-length genomes labeled in turquoise. The emergence of CRF50_A1D in Britain is dated to 1992.</p

Recombinant map of CRF50_A1D and maximum likelihood phylogenetic trees of non-recombinant fragments.

<p>Maximum likelihood trees of putative non-recombinant fragments from specimens 33365, 8179, 40534 and 34567 drawn using PhyML with PAUP-defined parameters. HIV-1 subtypes used for analysis were A–D, F, G, H, J, K. Numbers indicate bootstrapping support from 1000 replicates (excepting slice 5; 100 replicates). 70% bootstrap support and monophyletic clustering were the criteria for subtype classification. The recombinant map was drawn using the RDT program at Los Alamos. Component subtype fragments are labeled 1–9 on the genome map, corresponding with numbered phylogenetic trees. The genomic regions in which the URF specimen 34567 did not cluster with the CRF50_A1D specimens are indicated in the appropriate trees.</p

jpHMM analysis of six recombinant HIV-1 sequences.

<p>Putative recombinant HIV-1 sequences were submitted to the online implementation of jpHMM at the GOBICS server. The program used its own stored reference alignment and statistical algorithm to determine subtype classifications, breakpoint locations and 95% confidence intervals. Breakpoint locations and confidence intervals are marked on each plot and are equivalent to HXB2 numbering. In each plot, subtype A1 is represented in red, subtype A2 in coral (plot d only), subtype D in lavender, and subtype B in blue (plot d only). Areas of subtype uncertainty are grey. Five specimens (a, b, c, e, and f) showed largely identical A1/D structures, whereas one specimen (d) showed a complex A1/A2/D/B/U structure. a) Specimen 33365; b) Specimen 8179; c) Specimen 40534; d) Specimen 34567; e) Specimen 11762; f) Specimen 12792.</p

jpHMM-assigned breakpoint locations (with 95% confidence intervals) for five HIV-1 A1/D recombinant sequences^{^a}.

<p>^a Breakpoint locations as determined by jpHMM with HXB2 numbering. The breakpoint locations are generally consistent across the five specimens, indicating that the same A1/D recombinant structure is shared.</p><p>This corresponds to a region of subtype D uncertainty;</p><p>This corresponds to a region of subtype A uncertainty; refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083337#pone-0083337-g001" target="_blank">Figure 1</a>. PR = Protease.</p