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

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

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

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

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