Evidence of multiple transmission events during pediatric HIV-1 subtype C infection.

<p>Phylogenetic and sequence analysis of plasma and CSF HIV-1 populations for subject 3002. (a) Neighbor-joining tree. Sequences from the CSF are labeled with solid blue circles, and plasma sequences (PL) are labeled with solid red triangles. Bootstrap values ≥40 are indicated (<b>*</b>) at the appropriate nodes. Genetic distance is scaled at the bottom of the figure (0.001) and indicates the number of nucleotide substitutions per site between <i>env</i> sequences. The subject's age is noted, as well as the overall TMRCA and the TMRCA of the two transmitted viruses. The CNS sequestered population is represented by an open black circle. (b) Highlighter plot of aligned <i>env</i> plasma and CSF sequences, generated at <a href="http://www.hiv.lanl.gov" target="_blank">www.hiv.lanl.gov</a>. The HXB2 nucleotide position number is indicated on the <i>x</i> axis, and the sequence identifier is indicated on the <i>y</i> axis. Nucleotide changes are indicated by the following ticks on the highlighter plot: A, green; T, red; G, orange; and C, blue. The two transmitted populations are separated by a heavy black line.