Genetic characterization of accessory genes from human immunodeficiency virus type 1 group O strains.

Human immunodeficiency virus type 1 (HIV-1) group O strains have been described as highly divergent, compared with the vast majority of the viruses involved in the worldwide AIDS pandemic, classified in group M. To gain new insights into the diversity and genetic characteristics of group O, we have sequenced the accessory gene region (from vif to vpu) of 14 isolates. Analyses of the deduced amino acid sequences for Vif, Vpr, the first exon of Tat, and Vpu indicate that most of the functional domains of these proteins, as described for group M viruses, are highly conserved and retained among all the group O strains we have characterized. The only difference concerns the Vif phosphorylation sites, which are absent in all of the group O isolates we have sequenced; in contrast, they are well conserved in nearly all of the group M isolates, in which they play critical roles in the regulation of viral replication and infectivity. As already observed for group M isolates, the Vpu protein is also highly diverse among group O strains. Phylogenetic analyses of these sequences indicate that HIV-1 group O can be separated into four different clusters, containing most of the strains we have characterized (except one, which clusters outside of the analyzed viruses). Taking into account the criteria used for clades in group M, we were not able to define group O clades definitively.

HLA class I diversity among rural rainforest inhabitants in Cameroon: identification of A*2612-B*4407 haplotype.

The population distribution of alleles of the classical HLA class I loci in Cameroon has not been well studied but is of particular interest given the AIDS and malarial epidemics afflicting this population. We investigated the genetic diversity of HLA-A, HLA-B and HLA-C alleles in remote populations of Cameroon. Subjects from seven small, isolated, indigenous populations (N = 274) in the rainforest of southern Cameroon were typed for HLA-A, HLA-B and HLA-C alleles using a polymerase chain reaction/sequence-specific oligonucleotide probe assay and sequence analysis. Multiple alleles of the HLA-A (N = 28), HLA-B (N = 41) and HLA-C (N = 21) loci were identified, of which A*2301[allele frequency (AF) = 12.8%], B*5802 (AF = 10.9%) and Cw*0401 (AF = 16.6%) were the most frequent individual alleles and A*02 (AF = 19.0%), B*58 (AF = 15.9%) and Cw*07 (AF = 22.4%) the most common serologically defined groups of alleles. Twenty-six (28.9%) alleles with a frequency of less than 1% (AF < 1%), 39 (43%) with a frequency of 2.0-15.0% (AF = 2.0-15.0%), three globally uncommon alleles [A*2612 (AF = 2.0%), B*4016 (AF = 0.7%) and B*4407 (AF = 1.4%)], and the A*2612-Cw*0701/06/18-B*4407 haplotype (haplotype frequency = 1.3%) were also identified. Heterozygosity values of 0.89, 0.92 and 0.89 were determined for HLA-A, HLA-B and HLA-C, respectively. The extensive allelic and haplotypic diversity observed in this population may have resulted from varied natural selective pressures on the population, as well as intermingling of peoples from multiple origins. Thus, from an anthropologic perspective, these data highlight the challenges in T-cell-based vaccine development, the identification of allogeneic transplant donors and the understanding of infectious disease patterns in different populations.