Stratification of cohort into HIV-1 disease progression groupings.

1<p>CD4+ T cell decline without adjusting for first CD4 count and age of the participant.</p>2<p>CD4+ T cell decline after adjusting for first CD4 count and age of the participant.</p><p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-t001" target="_blank">Table 1</a> illustrates the stratification of 110 chronically HIV-1 adults into distinct progression groups. Six-monthly retrospective CD4 counts were used in a multilevel regression model to derive individual participant CD4 slopes. The slopes were calculated over a median observation time of 610 months (minimum-maximum 18–97 months). Annual CD4+ T-cell changes are expressed as medians with interquartile ranges. Positive (+) symbols indicate increasing CD4+ counts while (−) indicates decreasing CD4+ counts over time. Individuals in the extreme stratification group 1 were selected as rapid progressors (RP, n = 7) while those in group 5 were selected as slow progressors (SP, n = 14). Groups 2, 4and 4 were categorised as normal progressors (NP, n = 89). Normal progressors were those with CD4 slopes between −91/year to +10/year; RPs had CD4 slopes <−91/year while SPs had CD4 slopes >+10/year.</p

Evaluation of relationship between HIV disease progression and viral loads.

<p>CD4 slopes were computed by multilevel regression modelling of six-monthly retrospective participant CD4 counts. The median observation time over which CD4 slopes were calculated was 61 months (minimum 18 and maximum 97) months. Plasma viral load was quantified using Bayer™ bDNA assay according to the manufacturer's protocol; the plasma viral load minimum detection threshold was 50 RNA copies/ml. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g001" target="_blank">Figure 1A</a> illustrates the relationship between CD4 slopes and viral loads, ○denotes RPs, • are NPs; while ⊙are SPs; 1B compares mean viral loads between groups while <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g001" target="_blank">figure 1C</a> compares plasma viral loads in SPs who had HLA alleles known to be protective as previously described and to those who did not. The lines running parallel to the Y and X axis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g001" target="_blank">figures 1A and 1B</a> respectively) indicate the minimum detection limit for evaluation of plasma viral loads. For purposes of statistical analyses and graphical representation of the data, undetectable plasma viral loads were assumed to equate to 45 RNA copies per ml.</p

Distribution of Gag T-cell recognition among slow progressors.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g004" target="_blank">Figure 4</a> illustrates the frequency of Gag T-cell recognition across the p17, p24 and p15 Gag region among the slow progressors. The frequency is presented as the proportion of SP individuals with Gag T cell recognition. The horizontal axis represents the peptides recognised.</p

Relationship between multiclade Gag T-cell recognition and HIV disease progression.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g005" target="_blank">Figure 5</a> illustrates the total magnitudes of HIV Gag-induced IFNγ responses evaluated using ELISpot assay. A test was considered positive when response was ≥50 SFU/million PBMCs and at least twice the mean background response (6 wells of cells and media response only). The data is presented as net response; all background values have been subtracted. For purposes of statistical analysis and graphical representation, all negative responses (less than 50 net SFU/million PBMCs) were equated to zero SFU/ml PBMCs. Because the Y axis is presented in log, negative responses are not represented on these graphs. The X-axis represents individual participants. The horizontal dotted lines parallel to the X-axis represent the cutoff for a positive response. Slow progressors (SPs) are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g005" target="_blank">figure 5A</a>; rapid progressors (RPs) are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g005" target="_blank">figure 5B</a> while normal progressors are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g005" target="_blank">figure 5C</a>.</p

Breadth of HIV-induced IFN-γ T-cell recognition.

<p>The peptides sets evaluated were dictated by availability from the NIH AIDS reagent programme; clades A, B, C and D Gag peptides were obtainable while only clade B was available for Nef, Tat, Rev, Vif, Vpr, Pol and Vpu proteins. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g003" target="_blank">Figure 3</a> compares the proportion of participants (%) inducing HIV-specific IFN-γ responses using clade B peptides only, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g003" target="_blank">figure 3A</a>; as opposed to multiple clade Gag peptide sets, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-g003" target="_blank">figure 3B</a>.</p

Study population demographics, host genetics and multi-clade gag recognition.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004188#pone-0004188-t002" target="_blank">Table 2</a> illustrates study participant demographics and IFNγ response to clades A, B, C and D gag peptides. CD4+ T –cell slopes were derived from multilevel regression analysis of retrospective 6-monthly CD4+ T-cell counts. Under annual CD4 slope, symbol (−) indicates model-derived decreasing CD4 slopes while (+).indicates decreasing CD4 slopes over time. Under Gag-induced IFN-γ, areas marked + indicate induction of Gag-induced IFN-γ responses to the respective clade of Gag peptides, blank areas indicate lack of IFN-γ response. Clade of the infecting HIV virus was determined from partial sequences of the Gag region, “nd” indicates not done. Bold highlights indicate HLA alleles that have been reported to confer protection from HIV disease.</p

Sexual behavior scores (SBSs) across visits for study groups in the UK¹ (top row) and Uganda (bottom row) cohorts.

<p>Boxplots of SBSs of concordant individuals are shown, where the midline and box represent the median ± the 25th and 75th percentiles; whiskers extend to the extreme data points that are ≤1.5 times the interquartile range. Extreme outliers are indicated by circles. ¹Note that the scales of the y-axis for UK HIV+ and HUSN are much larger than those of the other groups. *One UK HESN with a very large SBS at Visit 3 (0.126) is not shown in order to maintain a comparable scale over plots where possible.</p

Risk indexes (RIs) for HESN participants in the UK and Ugandan cohorts over 4 visits.

<p>RIs were generated based on reported sexual behaviors for the last 3 months (if concordant with answers from the HIV+ study partner), partner HIV-1 pVL, concurrent STIs, male circumcision status, and pregnancy. Boxplots of RI are shown, where the midline and box represent the median ± the 25th and 75th percentiles; whiskers extend to the extreme data points that are ≤1.5 times the interquartile range. Extreme outliers are indicated by circles.</p

Data from visit 1 summarising key sexual behavior acts (with ejaculation and no condom use) reported within the past 3 months and the proportion of couples who were concordant in their responses across all sex acts.

a<p>NR; none reported.</p>b<p>Single data point only.</p

Summary of Study Group Characteristics for UK and Uganda.

a<p>IQR; Interquartile range.</p>b<p>No participants self-identified as bisexual, therefore those not identified as MSM are heterosexual.</p>c<p>Participants positive for Chlamydia, Gonorrhoea, GUD, Bacterial Vaginosis, Candidiasis, and/or Syphilis at any study visit, and/or reporting incidences of genital lesions/discharge/rash/itching in the 3 months preceding any study visit.</p>d<p>No pVL data available for one UK and one Ugandan HIV+ participant at visit 1.</p>e<p>Limit of detection 50 copies/ml in UK and 400 copies/ml in Uganda samples.</p>f<p>No CD4+ count data for one UK HIV+ participant at visit 1.</p