title: Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil.
abstract: Sequence analysis of a human immunodeficiency virus type 1 env gene PCR amplified from a Brazilian woman's peripheral blood mononuclear cell DNA (sample RJIO1) showed that it was likely to have been derived from a double recombination event between human immunodeficiency virus type 1 subtypes B and F. The major portion of the gp120 coding sequence belonged to the B lineage, but a segment of the C2 to V3 region (approximately 135 nucleotides) clearly associated with sequences of the F lineage. The subtype F-like segment had 15 noncontiguous signature nucleotides in common with Brazilian subtype F sequences that were not found, or were rare, in subtype B sequences. In contrast, this same segment had only 3 signature nucleotides shared with subtype B sequences and not present in the Brazilian subtype F sequences. Phylogenetic analysis, amino acid signature pattern analysis, and the pattern of synonymous mutations all supported the hypothesis of a recombinational origin of the RJIO1 sequence. Related recombinant genes were also detected in peripheral blood mononuclear cell DNA obtained from the woman's recent sexual partner, indicating that the recombination event probably occurred at some previous time in the chain of virus transmission. Divergent viral sequences in the V3 region were found in the male sexual partner, while a relatively homogeneous viral population was detected in the woman, consistent with her recent infection.
authors.affiliation: Irwin Memorial Blood Centers, San Francisco, California 94118.
authors.forename: E C
authors.initials: EC
authors.lastname: Sabino
authors.forename: E G
authors.initials: EG
authors.lastname: Shpaer
authors.forename: M G
authors.initials: MG
authors.lastname: Morgado
authors.forename: B T
authors.initials: BT
authors.lastname: Korber
authors.forename: R S
authors.initials: RS
authors.lastname: Diaz
authors.forename: V
authors.initials: V
authors.lastname: Bongertz
authors.forename: S
authors.initials: S
authors.lastname: Cavalcante
authors.forename: B
authors.initials: B
authors.lastname: Galvão-Castro
authors.forename: J I
authors.initials: JI
authors.lastname: Mullins
authors.forename: A
authors.initials: A
authors.lastname: Mayer
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000453:epidemiology / Q000382:microbiology*; D000595:Amino Acid Sequence; D001483:Base Sequence; D001938:Brazil / Q000453:epidemiology; D017931:DNA Primers; D005260:Female; D015686:Gene Products, env / Q000737:chemistry / Q000235:genetics*; D015752:Genes, env; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D011995:Recombination, Genetic; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017931:DNA Primers; D015686:Gene Products, env; D015699:HIV Envelope Protein gp120