title: Evaluation of HIV type 1 group O isolates: identification of five phylogenetic clusters.
abstract: HIV-1 group O strains have a level of genetic diversity similar to that of strains in group M; however, group O has not been readily classified into genetic subtypes. Phylogenetic classification of group O has been hindered by the limited sequence information available. To facilitate phylogenetic analysis, we sequenced the gag p24 (693 nt), pol p32 (864 nt), and env gp160 (approximately 2700 nt) genes from 39 group O-infected specimens. These specimens include 32 plasma samples collected in Cameroon between 1996 and 1999, 2 specimens collected in the United States, and 5 infections previously isolated in Equatorial Guinea. Phylogenetic analysis of HIV-1 group O sequences resulted in the identification of five clusters that are maintained across gag, pol, and env, generally supported by high bootstrap values, and approximately equidistant from each other. In addition to the group O clusters, several isolates branch independently and are equidistant from the other group O isolates. Cluster I comprises greater than 50% of the group O isolates and is a diverse set of isolates that is subdivided into subclusters. The average intra-, sub-, and intercluster distances for group O are similar to the corresponding distances for group M subtypes. The five group O clusters have characteristics similar to those of group M subtypes. Thus the data presented may form the basis for classification of group O into subtypes. However, full-length genomes representing each group O cluster will be required to formalize a group O subtype classification.
authors.affiliation: Abbott Laboratories, Abbott Park, Illinois 60064, USA.
authors.forename: Julie
authors.initials: J
authors.lastname: Yamaguchi
authors.forename: Ana S
authors.initials: AS
authors.lastname: Vallari
authors.forename: Priscilla
authors.initials: P
authors.lastname: Swanson
authors.forename: Pierre
authors.initials: P
authors.lastname: Bodelle
authors.forename: Lazare
authors.initials: L
authors.lastname: Kaptué
authors.forename: Charlotte
authors.initials: C
authors.lastname: Ngansop
authors.forename: Leopold
authors.initials: L
authors.lastname: Zekeng
authors.forename: Lutz G
authors.initials: LG
authors.lastname: Gürtler
authors.forename: Sushil G
authors.initials: SG
authors.lastname: Devare
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Brennan
mesh_terms: D000595:Amino Acid Sequence; D002163:Cameroon; D015752:Genes, env; D015750:Genes, gag; D015751:Genes, pol; D016701:Guinea; D015699:HIV Envelope Protein gp120 / Q000737:chemistry; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017386:Sequence Homology, Amino Acid; D014481:United States
chemical_list: D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments