FIG. 4.

Neighbor-joining phylogenetic tree of V2-V5 sequences from superinfection cases. Reference sequences for subtype G, D, C, and A from the Los Alamos HIV database (http://www.hiv.lanl.gov/content/index) are displayed in black. Sequences from each subject are denoted in a separate color. For reference, sequences that were originally obtained from these cases using primers that amplify a subgenomic portion of envelope (V1-V5) (7, 38) are shown in italics. The case reference sequences were obtained from the first time point at which the superinfecting variants were detected and contain representatives of both the initial and superinfecting strains, except for case QD022, in which the superinfecting variants completely replaced the initial variants. Thus, the QD022.A and QD022.B initial sequences in bold italics were from a presuperinfection time point (0.14 ypi). Sequences from the full-length env clones from these same individuals isolated as part of this study are shown in bold print, with an asterisk denoting a superinfecting sequence and a caret denoting a sequence from the initial virus population, as defined in the previous study. Full-length envelope sequences were cloned either directly from PBMC DNA (subjects QA013, QB726, and QA413) or from PBMC DNA following short-term coculture with uninfected PBMCs (subjects QB008 and QD022) from the first time point at which superinfecting sequences were detected.