title: Phylogenetic analysis of 49 newly derived HIV-1 group O strains: high viral diversity but no group M-like subtype structure.
abstract: We assess the genetic relationships between 49 HIV-1 group O strains from 24 and 25 patients living in Cameroon and France, respectively. Strains were sequenced in four genomic regions: gag (p24) and three env regions (C2-V3, gp41, and for 22 C2-gp41). In each of the genomic regions analyzed, the genetic diversity among the group O strains was higher than that exhibited by group M. We characterize three major group O phylogenetic clusters (O:A, O:B, and O:C) that comprised the same virus strains in each of the genomic regions analyzed. The majority of strains cluster in O:A, a cluster previously identified by analysis of pol and env sequences. Group O recombinants were also identified. Importantly, the distinction between these three major group O clades was weak compared to the strong clustering apparent in the global group M phylogenetic tree that led to the identification of subtypes. Thus, these clusters of group O viruses should not be considered as equivalent to the group M subtypes. This difference between the pattern of group O and the global group M diversity, both taking into account the pandemic status of the group M subtypes and the comparatively small number of group O-infected individuals (the majority being from Cameroon), indicates that the group O phylogeny primarily represents viral divergence in the Cameroon region, analogous to group M viral diversity present in the Democratic Republic of Congo.
authors.affiliation: Service de Neurovirologie, CEA, Fontenay-aux-Roses, France. p.roques@cirmf.sci.ga
authors.forename: P
authors.initials: P
authors.lastname: Roques
authors.forename: D L
authors.initials: DL
authors.lastname: Robertson
authors.forename: S
authors.initials: S
authors.lastname: Souquière
authors.forename: F
authors.initials: F
authors.lastname: Damond
authors.forename: A
authors.initials: A
authors.lastname: Ayouba
authors.forename: I
authors.initials: I
authors.lastname: Farfara
authors.forename: C
authors.initials: C
authors.lastname: Depienne
authors.forename: E
authors.initials: E
authors.lastname: Nerrienet
authors.forename: D
authors.initials: D
authors.lastname: Dormont
authors.forename: F
authors.initials: F
authors.lastname: Brun-Vézinet
authors.forename: F
authors.initials: F
authors.lastname: Simon
authors.forename: P
authors.initials: P
authors.lastname: Mauclère
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000595:Amino Acid Sequence; D002163:Cameroon; D005260:Female; D005602:France; D015752:Genes, env / Q000235:genetics; D014644:Genetic Variation; D016655:HIV Core Protein p24 / Q000737:chemistry / Q000235:genetics; D015699:HIV Envelope Protein gp120 / Q000737:chemistry / Q000235:genetics; D015700:HIV Envelope Protein gp41 / Q000737:chemistry / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D007223:Infant; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012703:Serotyping
chemical_list: D016655:HIV Core Protein p24; D015699:HIV Envelope Protein gp120; D015700:HIV Envelope Protein gp41; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments