Many independent isolates of replication-competent HIV-1 have identical sequences. Phylogenetic trees of env sequences of independent isolates of replication-competent virus from each subject (n = 12). Sequencing was performed on genomic viral RNA in supernatants of p24⁺ wells. Cultures were established at limit dilution for viral outgrowth. Isolates containing more than a single sequence as indicated by double peaks at one or more positions in the chromatograms were not further analyzed. Symbols indicate the number of PHA stimulations after which the isolate was obtained. Sets of isolates with identical env sequences are boxed. Representative isolates obtained after different numbers of stimulations (arrows) from randomly selected sets were subjected to full-length sequencing at the single-genome level (see Fig. 4).