title: Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba.
abstract: BG intersubtype recombinants represented 11.6% of HIV-1 isolates in a recent survey in Cuba based on pol sequences, most of them forming a single clade further subdivided into 3 subclades. Here, we analyze 8 near full-length genomes and 1 gag-pol sequence from epidemiologically unlinked Cuban BG recombinants from these 3 subclades (3 from each). Near full-length sequences were also obtained from 3 subtype G and 2 subtype B Cuban viruses. Phylogenetic relationships were estimated via maximum likelihood, and mosaic structures of the recombinants were inferred with the bootscanning, MaxChi, Genconv, and GARD methods. For the near full-length genomes, all recombinants formed a strongly supported clade further subdivided into the same subclades previously defined in pol. Mosaic structures were identical within each subclade and different among subclades, although 5 breakpoints were coincident among all recombinants. Individual phylogenetic trees for nonrecombinant fragments (concatenated B and G subtype segments) indicated a common ancestry for the parental viruses and their relationships to local subtype B and G strains. These results allow us to identify 3 new BG intersubtype circulating recombinant forms in Cuba derived from a common recombinant ancestor, which originated from B and G subtype parental strains circulating in Cuba.
authors.affiliation: Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: María
authors.initials: M
authors.lastname: Sierra
authors.forename: Michael M
authors.initials: MM
authors.lastname: Thomson
authors.forename: David
authors.initials: D
authors.lastname: Posada
authors.forename: Lissette
authors.initials: L
authors.lastname: Pérez
authors.forename: Carlos
authors.initials: C
authors.lastname: Aragonés
authors.forename: Zoila
authors.initials: Z
authors.lastname: González
authors.forename: Jorge
authors.initials: J
authors.lastname: Pérez
authors.forename: Gema
authors.initials: G
authors.lastname: Casado
authors.forename: Rafael
authors.initials: R
authors.lastname: Nájera
mesh_terms: D001483:Base Sequence; D003462:Cuba / Q000453:epidemiology; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics; D013997:Time Factors