FIG. 3.

Phylogenetic analyses of defective HCV genomes. Nucleotide sequence data from 33 isolates from patient K4 were used for phylogenetic analyses. The defective HCV genome (16 isolates) and the nondefective HCV genome coexisting before interferon treatment (9 isolates; GenBank accession no. AB492219 to AB492227) and those after treatment (8 isolates; GenBank accession no. AB492228 to AB492235) were compared in the 5′ and 3′ maximum overlapping regions separately (5′-K4 and 3′-K4 in Fig. 2A). Phylogenetic trees were created for the respective regions (A and B). In the isolate designations, pre and af24 stand for before and after interferon treatment and S and L stand for defective and nondefective HCV genomes, respectively. Isolates with the same deletion pattern (according to K4-pre in Fig. 2) are shaded in the same color. Asterisks denote the representative isolates illustrated in Fig. 2.