Phylogenetic analysis of the RT region; details of the analysis are the same as for Fig. 1. Nucleotide alignment was based on the protein alignment in Fig. 4. (a) Tree based on sequences from BCM. (b) Subtree of patient and victim sequences, including those added by MIC. In both a and b, the smaller set of boxed sequences represents the sequences from the victim, and the larger set of boxed sequences represents the patient plus victim sequences. The victim sequences were found to be embedded within the patient sequences in all analyses and for all models of evolution examined. In addition to the 100% bootstrap support of this relationship for the minimum evolution analyses, the parsimony bootstrap support was 96% and the Bayesian posterior support was 100%.

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