Isolates with identical sequence are part of more complex proviral populations reflecting diversification over time during chronic infection. Limiting dilution analysis of proviruses present in resting CD4⁺ T cells was performed on cells from three representative patients from whom sets of identical isolates of replication-competent virus were obtained. The V3-V4 region of env was sequenced, and the resulting sequences (open circles) were used in phylogenetic analysis along with the replication-competent isolates (closed symbol; shapes reflect the number of PHA stimulation as in Fig. 3). Sets of identical independent sequences are boxed.