Methods

PR alleles were amplified from plasma RNA or from peripheral blood mononuclear cell DNA from samples collected at entry, after 24-32 weeks of therapy, and at two intermediate time. points. Amplified products of about 1.7 kb, which extended from CA in the gag region through PR and into RT in the pol region (see Fig. 2B), were cloned so that sequences could be determined for individual PR alleles. Nucleotide sequences from five to ten clones at each time point were merged and translated in Gene Runner 3.0 for Windows© (Hastings Software Inc., 1994). Sequences were aligned using COMPARE in the DNA sequence alignment editor 2.4 (Dr. Alan Goldin, Department of Biology, Cal Tech, 1994). Phylogenetic analysis was performed using neighbor] oining and Kimura two-parameter distance matrix software in the PHYLIP package.26 Bootstrap analysis, based on 100 bootstrap trees, was performed to determine the confidence levels of branching, and branch values were superimposed on the neighbor-joining trees. Trees were constructed in the program TREEVIEW version 1.40 and further refined in Harvard Graphics version 1.03 (Software Publishing, 1992).

FIGURE 5. Clinical response in children during protease inhibitor therapy. Clinical response to therapy was monitored in three patients (A, upper panel; B, middle panel; and D, lower panel) by measuring log10 change from baseline of HIV-1 plasma RNA copies per milliliter (left y axis) and CD4 T cells per microliter (right y axis) over time (xaxis). Symbols: open, plasma RNA; closed, absolute CD4 T cell count.

FIGURE 5. Clinical response in children during protease inhibitor therapy. Clinical response to therapy was monitored in three patients (A, upper panel; B, middle panel; and D, lower panel) by measuring log10 change from baseline of HIV-1 plasma RNA copies per milliliter (left y axis) and CD4 T cells per microliter (right y axis) over time (xaxis). Symbols: open, plasma RNA; closed, absolute CD4 T cell count.

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