Based on anti-HIV-1 screening of a repository of 200,000 blood donor sera collected in late 1984, the Transfusion Safety Study identified and enrolled into ongoing followup 133 seropositive donors and 111 HIV-1-infected transfusion recipients. Included among these were 38 'transmission clusters' composed of a donor and from one to six linked, infected recipient(s), and, in four cases, infected recipients' sexual partners. Frozen cells and sera collected at six-month intervals over a six-year period from members of these clusters were available for study. Specimens were accessed such that sub-repositories of cellular DNA, PCR-amplified HIV-1 sequences, and viral isolates were generated for future investigations of these unique clusters. The studies included analysis of sequence diversity in envelope (env) V3, V4, and V5 hypervariable regions both within each infected individual over time, and between different members of each cluster and different clusters. Sequence diversity profiles from PBMC and serum were analyzed separately to discern differences in these different blood components at each sampling and over time. The pattern of turnover of specific sequence variants over time (evolution of viral genotypes) was correlated with clinical and immunological progression.