FIG. 2.

Analyses of reinfection in subject QB008. (a) Plasma viral loads and results of HIV-1 sequence analyses at various times p.i. both HIV-1 antibodies and RNA were detected 121 days after the subject tested HIV-1 RNA negative and seronegative. Thus, the date of infection was estimated as the midpoint between the two visits. The layout for this figure is as described in the legend for Fig. 1a. (b) Bootscan analyses of representative initial (QB008.129.A3) and reinfecting clones (QB008.591.A1). The day p.i. from which the clone was obtained is indicated in the clone name, after the subject designation. The percentage of permuted trees is shown versus the sequence position. Recombination with less than 70% bootstrap support was considered to be statistically insignificant. The reference strains that were used in the analysis are indicated to the right and are given a color. A phylogenetic tree of the sequence is shown; in the case of the virus QB008.591.A1, which had a clear breakpoint in the bootscan analysis, the sequences from before and after that breakpoint were analyzed individually. The subtype designation is shown schematically at the bottom of each bootscan. (c) Results of subtype-specific PCR of PBMC DNA (top) and culture DNA (bottom). The layout is as described in the legend for Fig. 1c.