title: Near full-length genomes of 15 HIV type 1 group O isolates.
abstract: Human immunodeficiency virus type 1 (HIV-1) is classified into three distinct groups; M (major), N (non-M/non-O), and O (outlier). Group M strains are further subclassified into subtypes, subsubtypes, and circulating recombinant forms (CRF). While the level of genetic diversity within group O is similar to that between group M subtypes, group O has not been classified into subtypes. A previous study, based on the phylogenetic analyses of the gag p24, pol p32, and env gp160 sequences from 39 group O isolates, laid the foundation for the classification of group O subtypes. Five phylogenetic clusters, I-V, were identified that have characteristics analogous to group M subtypes. However, a complete phylogenetic analysis and classification of group O requires the availability of at least two full-length and one partial genomes for each group O phylogenetic cluster. In this study, 15 group O isolates were selected for full genome sequencing. Phylogenetic analysis of the 15 sequences with eight additional group O genomes supports the classification of three group O subtypes (I-III) and the potential existence of one CRF (IV) and at least one additional subtype (V). The group O subtypes are equidistant to each other and lack subsegments of other subtypes. The intra- and intersubtype genetic distances for group O are similar in magnitude to the corresponding distances for group M subtypes. Intersubtype recombination was identified in three of the 23 (13%) group O genomes. Formal classification of group O subtypes should be forthcoming pending the analysis of additional group O genomes and agreement of the HIV nomenclature committee.
authors.affiliation: Abbott Laboratories, Abbott Park, Illinois 60064, USA.
authors.forename: Julie
authors.initials: J
authors.lastname: Yamaguchi
authors.forename: Pierre
authors.initials: P
authors.lastname: Bodelle
authors.forename: Lazare
authors.initials: L
authors.lastname: Kaptué
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: D024882:Drug Resistance, Viral; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology; D016333:HIV Protease / Q000235:genetics; D017320:HIV Protease Inhibitors / Q000494:pharmacology; D015497:HIV-1 / Q000145:classification* / Q000187:drug effects / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D017320:HIV Protease Inhibitors; D016333:HIV Protease