Background:  Previous reports have indicated that APOBEC3G, a cytidine deaminase responsible for G-to-A hypermutation of HIV DNA, may be expressed at elevated levels in long-term non-progressors (LTNP). We have shown that some elite suppressors, a subset of LTNP who maintain undetectable viral loads in absence of treatment, harbor replication competent virus. Here, we investigate whether this innate immune response to HIV infection can control viremia in elite suppressors.

Methods:  A novel assay utilizing limiting dilution “digital” polymerase chain reaction (PCR) was devised to gauge the quality of the integrated provirus in the resting CD4⁺ latent reservoir. Unbiased primers lacking APOBEC3G recognition sites were targeted at an area of the HIV genome harboring elevated levels of hypermutation. Individual clones were directly sequenced and analyzed for evidence of hypermutation. Full-length vif sequence was obtained via direct sequencing of the low level plasma virus. APOBEC3G mRNA levels were measured using real-time PCR. In the infectivity assay, phytohemagglutinin (PHA) -activated resting CD4⁺ cells were infected with HIV-1 and kinetics were measured over a period of seven days.

Results:  A total of 978 proviral clones were analyzed in 8 elite suppressors and 9 HAART-treated patients. Our results indicate that elite suppressors have levels of hypermutation that are not significantly different from those in patients on HAART (19 vs 21%). In 1 patient (ES3), however, hypermutated sequences accounted for 80% of the integrated provirus, a statistically significant difference between this patient and the other patients in our study. While the vif sequence in ES3 did not have any novel or nonfunctional mutations, lab strain virus still replicated effectively in this patient’s CD4⁺ cells. We also demonstrate that mRNA levels of APOBE3G do not correlate with hypermutation levels.

Conclusions:  Hypermutation occurs in ~20% of provirus with significant patient to patient variability. Despite previous reports, our data indicate that hypermutation is not responsible for the control of viremia in the majority of elite suppressors. In these patients, suppression is probably mediated via a combination of other host and viral factors, including cytotoxic T lymphocyte responses. However, we cannot rule out the possibility that APOBEC3G contributes significantly to the control of viremia in ES3. Thus, APOBEC3G remains a target for possible therapeutic intervention.