title: Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro.
abstract: 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, gp120-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 gp120 gene was determined from each of 35 clones examined. Two of 13 (15%) PBMC-derived gp120 genes and 3 of 22 (14%) coculture-derived gp120 genes were defective as a result of frameshifts and an in-frame stop codon(s). Mean diversity between individual gp120-coding sequences in PBMC was fivefold greater (3.24%) than after coculture (0.65%). A predominant sequence of "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.
authors.affiliation: Department of Cancer Biology, Harvard School of Public Health, Boston, Massachusetts 02115.
authors.forename: K
authors.initials: K
authors.lastname: Kusumi
authors.forename: B
authors.initials: B
authors.lastname: Conway
authors.forename: S
authors.initials: S
authors.lastname: Cunningham
authors.forename: A
authors.initials: A
authors.lastname: Berson
authors.forename: C
authors.initials: C
authors.lastname: Evans
authors.forename: A K
authors.initials: AK
authors.lastname: Iversen
authors.forename: D
authors.initials: D
authors.lastname: Colvin
authors.forename: M V
authors.initials: MV
authors.lastname: Gallo
authors.forename: S
authors.initials: S
authors.lastname: Coutre
authors.forename: E G
authors.initials: EG
authors.lastname: Shpaer
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000382:microbiology*; D000328:Adult; D000595:Amino Acid Sequence; D001483:Base Sequence; D002478:Cells, Cultured; D003001:Cloning, Molecular; D004279:DNA, Viral / Q000235:genetics / Q000302:isolation & purification; D005814:Genes, Viral; D014644:Genetic Variation; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides; D016133:Polymerase Chain Reaction / Q000379:methods; D015183:Restriction Mapping; D012689:Sequence Homology, Nucleic Acid; D014759:Viral Envelope Proteins / Q000235:genetics*; D015678:Viral Structural Proteins / Q000235:genetics*
chemical_list: D004279:DNA, Viral; D009838:Oligodeoxyribonucleotides; D014759:Viral Envelope Proteins; D015678:Viral Structural Proteins