Genetic characterization of HIV before widespread testing of HIV vaccine candidates at a clinical trial site in Pretoria, South Africa

Identification and genetic characterization of unique HIV-1 A1/C recombinant strain in South Africa

HIV isolates from South Africa are predominantly subtype C. Sporadic isolation of non-C strains has been reported mainly in cosmopolitan cities. HIV isolate j51 was recovered from a rural South African heterosexual female aged 51 years. Near full length amplification of the genome was attempted using PCR with primers targeting overlapping segments of the HIV genome. Analysis of 5593 bp (gag to vpu) at a bootstrap value greater than 70% found that all but the vpu gene was HIV-1 subtype A1. The vpu gene was assigned HIV-1 subtype C. The recombination breaking point was estimated at position 6035+/- 15 bp with reference to the beginning of the HXB2 reference strain. Isolate j51 revealed a unique genome constellation to previously reported recombinant strains with parental A/C backbones from South Africa though a common recombination with subtype C within the vpu gene. Identification of recombinant strains supports continued surveillance of HIV genetic diversity.

Sustained favourable HIV viral load response in South African patients during concomitant HAART and cancer therapy

HIV infection has led to an increase of both AIDS defining and non-AIDS defining cancers. Immunosuppressive cancer therapy had been noted for increased HIV viral load in cancer patients infected with HIV before the advent of highly active antiretroviral therapy (HAART). Assessing the outcome of concomitant HAART and cancer treatment in regions endemic for HIV is thus important. From a cohort of 34 cancer patients infected with HIV, 10 (six underwent radiotherapy and four chemotherapy) had at least three serial samples collected before, during and after treatment. From each sample, HIV viral load, CD4 +  and CD8 +  cell count was investigated. HIV genotypic drug resistance was assessed for six patients with a detectable HIV viral load at baseline. Of the 10 patients; one was HIV positive only, three were HIV and HBV co-infected and six were HIV, HBV and HCV triple infected. Four patients were HAART experienced at recruitment, while six were HAART naive with detectable HIV viral loads. A significant HIV viral load decrease (P = 0.0128) was observed in all six patients with detectable baseline HIV viral loads. The four patients on HAART at recruitment maintained lower than detectable HIV viral load status throughout cancer therapy. A positive correlation between the rise in CD4 +  cell count and attaining a lower than detectable HIV viral load was also observed (P = 0.0439). This pilot study supports concomitant treatment of HIV/AIDS and cancer in HIV endemic regions irrespective of the type of cancer diagnosed, prescribed cancer therapy or other viral (HBV, HCV or both) co-infections.

Striking lack of T cell immunodominance in both a multiclade and monoclade HIV-1 epidemic: implications for vaccine development

Understanding the impact of HIV diversity on immunological responses to candidate immunogens is critical for HIV vaccine development. We investigated the reactivity and immunodominance patterns of HIV-1 consensus group M Gag and Nef in (i) Cameroon, where individuals infected with the predominant CRF02_AG clade were compared with those infected with diverse non-CRF02_AG clades; and (ii) in a multiclade epidemic, namely Cameroon, compared with a monoclade C epidemic, South Africa. We analyzed 57 HIV-infected individuals from Cameroon and 44 HIV-infected individuals from South Africa for differences in detecting HIV-1 consensus M Gag and Nef T cell responses using the IFN-γ ELISpot assay. We found no difference in the predicted epitope coverage between CRF02_AG and non-CRF02_AG viruses for either Gag or Nef. There were no differences in the magnitude and breadth of responses for CRF02_AG and non-CRF02_AG-infected individuals. In contrast, the specificity of epitope targeting was markedly different between the two groups, with fewer than one third (11/38) of peptides commonly recognized in Gag. Furthermore, only one peptide was commonly recognized by at least three individuals from both AG and non-AG groups, indicating poor immunodominance. For Nef, more than half of all targeted peptides (14/27) were recognized by both groups, and four peptides were commonly targeted by at least three individuals. Three times more peptides were exclusively targeted in the diverse non-CRF02_AG group compared to the CRF02_AG group (10 vs. 3). Of note, similar results were obtained when South Africa, a monoclade C epidemic, and Cameroon, a multiclade epidemic, were compared. The central nature of HIV-1 consensus M sequences resulted in their broad recognition, but failed to identify highly immunodominant peptides between homogeneous and diverse HIV epidemics.