Background:  APOBEC3G is an important innate immune molecule that causes HIV-1 hypermutation, which can result in detrimental viral genome mutations. The Vif protein of wild type HIV-1 counteracts APOBEC3G activity by targeting it for degradation and inhibiting its incorporation into viral particles. Additional APOBEC cytidine deaminases have been identified, such as APOBEC3F, which has a similar mode of action but different sequence specificity. A relationship has been proposed between APOBEC3G/3F and HIV disease progression. We hypothesized that hypermutation could be identified in a cohort of HIV-infected subjects from Nairobi, Kenya, and that this hypermutation could be correlated with clinical measures of HIV disease progression.

Methods:  Proviral DNA was isolated from 240 Kenyan women infected with HIV-1 from a high-risk commercial sex worker cohort, as well as a lower-risk group, and used as a template for sequencing the vpu gene and the first 349 nucleotides of env. Plasma RNA of this region and proviral vif was additionally sequenced for a subset of patients. The resulting sequences were examined for hypermutation. Where available, CD4 cell count was determined. Mann-Whitney and test for correlation statistical analyses were performed using GraphPad Prism 4.

Results:  Of the 240 that were examined, we identified 13 hypermutated proviral vpu/env sequences. Sequences derived from plasma virus, however, lacked hypermutation, as did proviral vif. When examining correlates of disease progression, subjects with hypermutated provirus were found to have significantly higher CD4 counts compared with the other subjects (p = 0.0052). Furthermore, hypermutation as estimated by elevated adenine content positively correlated with CD4 count for all the study subjects (p = 0.042). The sequence context of the observed hypermutation was statistically associated with APOBEC3G/3F activity.

Conclusions:  In contrast to previous studies, this study demonstrates that higher CD4 counts correlate with increased hypermutation in the absence of obvious mutations in the APOBEC inhibiting Vif protein. This strongly suggests that host factors such as APOBEC3G/3F are playing a protective role in these patients, modulating viral hypermutation and host disease progression. These findings support the potential of targeting APOBEC3G/3F for therapeutic purposes.