Phylogenetic Trees

Phylogenetic trees, which were constructed from all the nucleotide sequences in the dataset, established the epidemiological linkages among sequences from each patient and demonstrated the integrity of the dataset (Fig. 6). The virus populations in each child were distinct, which was expected, as none of the children who were infected by maternal transmission were siblings, nor were hemophiliac patients infected by the same blood products. The relationship among viruses from treated individuals was essentially identical among untreated children and their mothers.7 In

FIGURE 6. Phylogenetic tree of protease nucle-otide sequences from five children treated with protease inhibitors. Letters next to branches identify patients. Patients A, B, and D are described in this chapter. The HIV LAI protease sequence was used as an outgroup in the generation of this tree.

addition, every PR sequence within each patient was different at the nucleotide level, indicating genetic complexity in the samples.

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