Nested-primer polymerase chain reaction (PCR) has been applied to the molecular cloning of 4.6-kb half-genome fragments of human immunodeficiency virus type 1 (HIV-1) taken directly from the peripheral blood mononuclear cells (PBMC) of an individual with neurological symptoms of HIV-1 infection. In a similar manner, gpl20-coding portions of the envelope gene were cloned after PBMC from the same blood sample were cocultivated with uninfected PBMC for 28 days. The complete 1.6-kb nucleotide sequence of the gpl20 gene was determined from each of 35 clones examined. Two of 13 (15%) PBMC-derived gpl20 genes and 3 of 22 (14%) coculture-derived gpl20 genes were defective as a result of frameshifts and an in-frame stop codon(s). Mean diversity between individual gpl20-coding sequences in PBMC was fivefold greater (3.24%) than after coculture (0.65%). A predominant sequence or "strain" was found after coculture that was distinct from the diverse viral genotypes detected in vivo and therefore was selectively amplified during in vitro propagation. Multiple distinct third variable (V3) regions encoding the principal neutralizing domain of the envelope protein were detected in PBMC-derived genes, suggesting the presence of immunologic diversity of HIV env genes in vivo not reflected in the cocultured virus sample. The large size of the HIV fragments generated in this study will permit analysis of the diversity of immunologic reactivity, gene function, and pathogenicity of HIV genomes present within infected individuals, including the functional significance of the loss of diversity that occurs upon coculture. * Corresponding author. t We wish to acknowledge the memory of our dear colleague Donald Vaughn Faulkner. Don launched and nurtured many of us into the computer age, and he is greatly missed.

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