title: Analysis of near full-length genome sequences of HIV type 1 BF intersubtype recombinant viruses from Brazil reveals their independent origins and their lack of relationship to CRF12_BF.
abstract: We analyze the recombinant structures and phylogenetic relationships of nine near full-length genome sequences of HIV-1 BF intersubtype recombinant viruses from Brazil, eight of them newly derived. These were obtained by PCR amplification from peripheral blood mononuclear cells (PBMCs) DNA or PBMCs culture supernantant RNA. The recombinants exhibited unique mosaic structures, except two viruses with a single near coincident breakpoint. Comparison with CRF12_BF revealed only two coincident breakpoints in two recombinants. Phylogenetic analyses failed to support a common ancestry of Brazilian recombinants or their relationship to CRF12_BF, which widely circulates in Argentina. Intersubtype breakpoint distribution along the genome was uneven, with the highest mean frequency in the polymerase domain of reverse transcriptase, and the lowest in env. These results indicate that HIV-1 BF recombinants from Brazil have independent origins and are unrelated to CRF12_BF, and that intersubtype breakpoints are frequent in pol segments analyzed for drug resistance detection.
authors.affiliation: Area de Patogenia Viral, Centro Nacional de Microbiología, Instituto de Salud Carlos III. Ctra. Majadahonda-Pozuelo, Km. 2. 28220 Majadahonda (Madrid), Spain. mthompson@isciii.es
authors.forename: Michael M
authors.initials: MM
authors.lastname: Thomson
authors.forename: María
authors.initials: M
authors.lastname: Sierra
authors.forename: Amilcar
authors.initials: A
authors.lastname: Tanuri
authors.forename: Silvia
authors.initials: S
authors.lastname: May
authors.forename: Gema
authors.initials: G
authors.lastname: Casado
authors.forename: Nuria
authors.initials: N
authors.lastname: Manjón
authors.forename: Rafael
authors.initials: R
authors.lastname: Nájera
mesh_terms: D001938:Brazil; D002478:Cells, Cultured; D004279:DNA, Viral / Q000032:analysis / Q000097:blood; D019143:Evolution, Molecular; D005260:Female; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000032:analysis / Q000097:blood; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral