title: High frequency of recombinant genomes in HIV type 1 samples from Brazilian southeastern and southern regions.
abstract: We describe the genetic variability of HIV-1 subtypes and recombinant genomes in samples from southeastern and southern Brazilian regions. Phylogenetic analysis of a subset of 34 samples (8F, 7B, 7C, 2D, 1A, and 9 B" variant) based on the DNA sequencing of the env gp120 and gp41, gag p17, and nef regions confirmed the presence of nine (26.5%) potentially HIV-1 recombinant genomes. From the eight C2-V3 gp120 subtype F samples, only two seem to be pure F. One of the samples, classified as B" in the C2-V3 gp120 and as B in gp41 had the gag and nef regions clustering with subtype C. Two of seven C2-V3 subtype C samples presented distinct recombinant patterns as Bgag/Cenv/Bnef and Bgag/Cenv/Cnef. Putative recombinant breakpoints were obtained for three samples presenting discordant subtypes (F/B) between gp120 and gp41 env fragments showing that similar breakpoints could be observed between two unlinked samples (95BRRJ014 and 96BRRJ101). A higher degree of polymorphism was verified in the analysis of a subtype A sample (98BRRS058) in the C2-V3/gp41 env fragment. The intrasubtype C distance was found to be lower than that found for the other subtypes for all genomic regions. These data confirm that distinct HIV-1 subtypes and recombinant forms are actively participating in the Brazilian AIDS epidemic, and that the subtype C was introduced more recently into southern Brazil.
authors.affiliation: Department of Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
authors.forename: Monick Lindenmeyer
authors.initials: ML
authors.lastname: Guimarães
authors.forename: Aline
authors.initials: A
authors.lastname: dos Santos Moreira
authors.forename: Regina
authors.initials: R
authors.lastname: Loureiro
authors.forename: Bernardo
authors.initials: B
authors.lastname: Galvão-Castro
authors.forename: Mariza Gonçalves
authors.initials: MG
authors.lastname: Morgado
mesh_terms: D001483:Base Sequence; D001938:Brazil; D005787:Gene Frequency; D016679:Genome, Viral; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D015700:HIV Envelope Protein gp41 / Q000235:genetics; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic
chemical_list: D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41