Results of different compartmentalization tests.

<p>Values are p-values obtained from randomization tests. P<0.05 was considered evidence of compartmentalization.</p>a<p>SM  =  Slatkin-Maddison.</p>b<p>r  =  Correlation coefficient by length of branches.</p>c<p>r_b  =  Correlation coefficient by number of branches.</p>d<p>AI  =  Association Index.</p>e<p>Snn  =  Nearest neighbor statistic.</p

Plasma and breast milk viral load.

<p>Viral loads determined by Roche Amplicor (PL) and Roche Amplicor Ultrasensitive (BM) assays. Gray lines are means.</p

CD4+ T cell count at time of study entry, viral load at sequence sample time, and number of unique gp160 sequences.

a<p>PL always sampled previous to BM.</p>b<p>BML  =  Milk from the Left Breast.</p>c<p>BMR  =  Milk from the Right Breast.</p

Maximum likelihood trees of region gp160, PL samples obtained previous to BM samples.

<p>All trees were calculated under the GTR+G+I model, rooted with 4 subtype C reference sequences obtained from LANL sequence database. In all subjects, HIV-1 RNA sequences from the left breast (white circles) and from the right breast (gray circles) were intermixed. The scale at the bottom left of each tree corresponds to the number of substitutions per site (for example, 0.01 = 1 substitution per 100 sites).</p

Maximum likelihood trees of region gp160, PL and BM samples obtained contemporaneously.

<p>All trees were calculated under the GTR+G+I model, rooted with 4 subtype C reference sequences obtained from LANL sequence database. In all subjects, HIV-1 RNA sequences from the left breast (white circles) and from the right breast (gray circles) were intermixed. The scale at the bottom left of each tree corresponds to the number of substitutions per site (for example, 0.01 = 1 substitution per 100 sites).</p

Alignment of MPER sequence variants from all subjects described in this study.

<p>Sequences are aligned against HXB2 and a subtype C consensus sequence derived from the 2007 LANL database. Numbering is based on HXB2. MSD denotes start of the Membrane Spanning Domain. Consensus residues are color-coded by degree of conservation (red >98%, orange 90–97.9%, yellow 75–89.9%, green <75%). In panel A, IC₅₀ for mAb 4E10 is expressed as a range for all functional clones tested for each MPER variant. Positions 677, 680, 683, and 686 are color-coded for emphasis. In Panel B, Env protein sequences have been color-coded according to charge at positions 677, 680, and 683 (blue = basically charged residue, yellow = uncharged residue). All other residues (in white) are uncharged.</p

Maximum-Likelihood phylogenetic tree of all <i>env</i> sequences used in this study.

<p>HXB2 is used as an outgroup to root the tree.</p

Binding ELISA results for subject 16Ms plasma.

<p>Binding ELISA testing subject 16Ms plasma against normal human plasma and four monoclonal antibodies for binding to two gp41 constructs, one full-length MPER peptide, and two control peptides.</p

Clinical characteristics of study subjects.

<p>*Transmission type established by timing of the infant's positive DNA PCR: <i>In Utero</i> Transmission (IUT) = HIV DNA positive at birth, Breast Milk Transmission (BMT) = HIV DNA PCR positive at >1 month with negative HIV DNA PCR results prior to that timepoint.</p

Diversity and divergence in breast milk and plasma.

<p>(<b>A</b>) Comparing mean diversity of virus in breast milk and plasma HIV-1 RNA gp160 sequences of contemporaneously sampled subjects. Triangles  =  plasma, circles  =  breast milk; star  =  significant difference between plasma and breast milk diversity, p-values from Wilcoxon rank sums test. (<b>B</b>) Comparing diversity in breast milk and plasma in all contemporaneously sampled patients in aggregate, using Gilbert, Rossini, and Shankarappa's method for comparing intra-individual genetic sequence diversity between populations. Black lines are means. (<b>C</b>) Comparison of mean divergence of virus in BM and PL within contemporaneously sampled subjects. P-values from Wilcoxon rank sums test. (<b>D</b>) Comparison of viral divergence between the BM and PL of all contemporaneously sampled subjects in aggregate. P-value obtained using a GEE model. Black lines are means.</p