Background: Human immunodeficiency virus type 1 (HIV-1) group O (outlier) was first identified in 1990 as an HIV-1 strain highly divergent from group M (major). 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 (5) phylogenetic clusters, I-V, were identified that are congruent across all 3 genes, supported by bootstrap values, and roughly equidistant from each other. The intra- and intercluster genetic distances for group O are similar in magnitude to the corresponding distances for group M subtypes. However, formal classification of group O requires the availability of at least two full-length and one partial genomes for each group O phylogenetic cluster.

Methods: In this study, 15 group O isolates were selected for full genome sequencing. The near full-length genomic sequences were obtained by PCR amplification of four segments that link the previously obtained gag, pol, and env fragments and include the LTRs.

Results: Phylogenetic analysis, using Phylip, of an alignment of these 15 sequences with 8 additional group O genomes supports the classification of 3 group O subtypes (I-III) and the potential existence of one circulating recombinant form (CRF) (IV) and at least one additional subtype (V). Each of group O clusters I, II, and III, is represented by 2 or more isolates with near full-length sequences and several partial genomes from additional isolates; the clusters are equidistant from each other and lack sub-segments of other clusters. Cluster IV is represented by 2 full and 1 partial genomes and may represent a CRF of group O; cluster IV is recombinant between cluster I and the parental strain of cluster IV. Cluster V also meets the subtype criteria except that only 2 isolates have been sequenced. Additional unclassified isolates suggest the existence of other group O subtypes. Intra- and intercluster recombination was identified in 5 of the 23 (22%) group O genomes.

Conclusions: Phylogenetic analysis of 23 genomic sequences provides strong evidence for group O subtypes. Formal classification of group O subtypes should be forthcoming pending the analysis of additional group O genomes and agreement of the HIV nomenclature committee.