The diversity of the infecting SHIV-162P3 inoculum.

<p>(A) A maximum likelihood tree constructed with 42 independent full-length clones isolated from the infecting SHIV-162P3 inoculum. An unrooted tree layout is displayed. The horizontal scale bar represents genetic distance. (B) Entropy plot of inoculum diversity as a function of nucleotide position.</p

Maraviroc susceptibilities of pseudoviruses with full-length T1 envelopes.

<p>In each graph, the percentages of inhibition relative to the extent of virus replication in the no-MVC control at various MVC concentrations are shown. The MVC susceptibilities of the following clones are shown: (A) Mac46–19, the most prevalent Mac46 day 14 env clone, (B) Mac463–20, a minority day 14 Mac46 env clone, (C) Mac73–34, the most prevalent day 21 Mac73 env clone, (D) Mac803–28, the most prevalent day 14 Mac80 env clone, (E) Mac803–30, a minority day 14 Mac80 env clone, (F) SHIV stock and CR02, the most prevalent env clones from the pre-infection SHIV-162P3 stock and day 14 control macaque CR02, respectively. Error bars represent the standard errors of the means of results from at least two experiments, each performed in triplicate. Nonlinear regression with a variable slope was used to estimate a fitted curve. MVC, maraviroc.</p

Phylogenetic analysis of T₁ and T₂ gp160 <i>env</i> sequences.

<p>Composite tree of 169 complete gp160 sequences that includes independent sequences isolated from the infecting SHIV-162P3 challenge stock and MVC-exposed and control macaques. Black star, SHIV-162P3 consensus <i>env</i> sequence; open stars, clonal SHIV-162P3 isolates; orange diamonds, day 14 Mac80; light green circles, day 21 Mac73; light blue squares, day 14 Mac46; red diamonds, day 70 Mac80; dark green circles, day 42 Mac73; dark blue squares, day 56 Mac46; grey triangles, day 14 control macaque CR02; black triangles, day 42 CR02; inverted black triangles, day 42 control macaque L375. Numerals indicate posterior probabilities of node support. The horizontal scale bar represents genetic distance.</p

Alignment of gp120 V3 and gp41 fusion peptide sequences obtained pre-challenge and from post-challenge time points 1 and 2.

<p>Independent clonal sequences isolated from three MVC-exposed, SHIV-162P3 infected macaques are shown. The pre-challenge sequences are the same for each macaque as they were derived from the SHIV-162P3 challenge stock. Predicted amino acid differences are shown and similarities indicated with dashes. The number of independent clones with the identical sequence is indicated to the left of each sequence. (A) Mac46, (B) Mac73, (C) Mac80. FP, fusion peptide.</p

The relationship between SHIV-162P3 stock full-length <i>env</i> obtained by standard cloning and single genome amplification.

<p>(A) An unrooted maximum likelihood tree constructed with standard clones and 17 previously reported sequences generated by single genome amplification. Blue circles, SGA clones; Yellow circles; standard clones. The horizontal bar represents genetic distance. (B) Highlighter plot indicates the gp160 nucleotide variation between clones. Clones are numbered sequentially; SGA clones are depicted with “sga” after the clone number. Adenine, green; Cytosine, aqua; Thymine, red; Guanine, orange. Grey bars indicate missing sequence.</p

SHIV Plasma Viral Loads in MVC-treated and comparator macaques.

<p>SHIV Plasma Viral Loads in MVC-treated and comparator macaques.</p

Upregulation of CD69 and CCR5 expression on CD16⁺ and CD16⁻ monocyte subsets.

<p>(A) PBMC from AIDS subjects were stained with fluorochrome-conjugated Abs. CD14 and CD16 expression identified three Mo subsets: CD14^highCD16⁻ (gate R2), CD14^highCD16⁺ (gate R3), and CD14^lowCD16⁺ (gate R4). (B) The frequency of each Mo subset was compared in AIDS (<i>n = 11</i>) and uninfected subjects (<i>n = 8</i>). The expression of CD69 (C) and CCR5 (D) was analyzed for each Mo subset from AIDS (<i>n = 9–11</i>) and uninfected subjects (<i>n = 5–9</i>). Median values are indicated as horizontal lines, and statistical significance in 6B–D was calculated using the Mann-Whitney test.</p

Distribution of patients with HAD and without neurocognitive impairment (NCI) stratified by plasma LPS levels.

<p>AIDS patients with CD4 counts <300 cells/µl were classified based on plasma LPS levels at one (n = 41) or two (n = 17) visits into 2 groups (cutoff 79 pg/ml, the median LPS value in the AIDS cohort). The distribution of patients with HAD or without NCI in these 2 groups was analyzed for statistical significance using the Chi-square test (p = 0.007) and odds ratio (3.8, with 95% confidence interval 1.403–10.7) with Prism4 software. The distribution of patients with MCMD and without NCI in the two groups was similar (p = 0.8).</p

Increased plasma LPS, sCD14, and CCL2 are associated with HAD.

<p>(A) Levels of LPS, sCD14, CCL2, and IL-6 were quantified in plasma of AIDS patients (n = 119) and uninfected controls (n = 25). (B) Spearman correlation (r and p-values) was calculated to determine the relationship between the LPS levels and sCD14, and between sCD14 and plasma CCL2 or IL-6. (C) Levels of plasma VL, CD4 counts, LPS, sCD14, CCL2, and IL-6 were compared in AIDS patients classified in 5 groups based on the degree of neurocognitive impairment (NCI) (None, No NCI; HAD, HIV-associated dementia; MCMD, minor cognitive and motor disorder; NPI-O, neuropsychiatric impairment due to conditions other than HIV; and ANI, asymptomatic NCI). Kruskal-Wallis test determined significant differences between the 5 groups in 1C. Median values in 1A and 1C are indicated as horizontal lines and significant differences between the 4 NCI groups <i>versus</i> the no NCI group (None) were determined using the Mann-Whitney test.</p

Monocytes are a minor reservoir for HIV replication compared to CD4+ T-cells <i>in vivo</i>.

<p>Highly pure CD4⁺ T-cells and total or CD16⁺ and CD16⁻ Mo subsets were sorted from the same donor peripheral blood sample by FACS from HIV-infected patients with (<i>n = 12</i>) or without (<i>n = 1</i>) AIDS. 8 of the 12 AIDS subjects had HAD. Levels of cell-associated (A) HIV DNA and (B) RNA were quantified by real time PCR and RT-PCR, respectively. (C) CD4⁺ T-cells and CD16⁺ or CD16⁻ Mo (10⁵ cells/well) from patients with high plasma VL were co-cultured with PHA/IL-2 activated Mo∶CD4⁺ T-cell co-cultures from HIV-uninfected subjects (Mo∶T-cell ratio of 1∶2; 0.5×10⁶ cells/well). Co-cultures were maintained up to 32 days and supernatants were recovered every 4 days. Shown are levels of HIV-p24 in supernatants quantified by ELISA at days 24, 28, and 32.</p