Background: The causes and results of intermittent low-level viremia (50–500 copies/ml) during HAART are not well understood. We address these issues using viral genetic analysis in the evaluation of children with viremia “blips” while on HAART.

Methods: Regions of pol encoding PR and RT and env (C2-V5 region) were amplified from the plasma and PBMC. Ten (10) or more amplicons were sequenced directly from end point dilutions of viral templates from multiple time points prior to and during HAART. Sequences were evaluated for the selection of drug resistant viral variants, phylogenetic relationships, distances from the most recent common ancestor (MRCA), and divergence between plasma and PBMC viral populations over the course of infection.

Results: Fourteen (14) children from our clinic with plasma sequence available agreed to participate in this observational study. Plasma from 43 episodes of intermittent viremia between 50 and 374 copies/ml during 1.6 to 6.3 yrs of HAART (median 4.1) was studied. Six (6) children had a single “blip” and 8 children had 2–10 “blips” (median 3.5). Viremia was detected in 3%–45% of RNA measurements (median 9.5%). A total of 119 PR, 104 RT, and 46 env sequences were amplified from plasma from 28 episodes of viremia from 10 children. New drug resistant viral variants were detected in only 1 subject, who had viremia in 32% of RNA measurements. Plasma env sequences were less diverse than PBMC virus for 6/6 subjects analyzed, and 4/6 had less divergence from MRCA compared to PBMC sequences. The 2 subjects with plasma virus that diverged from the MRCA more than PBMC had the 2 highest frequencies of viremia (32% and 45%). Selection of drug-resistant viral variants was detected in 1 of these subjects.

Conclusions: Genetic studies of HIV-1 in plasma during infrequent low-level viremia and in PBMC during years of effective HAART found that plasma HIV-1 had less diversity and less divergence from the MRCA compared to PBMC populations in most subjects. This pattern suggests the expression from a subset of HIV-1 infected cells. Less frequently and among subjects with frequent bouts of intermittent viremia, plasma virus diverged more than PBMC virus from the MRCA of infection, indicating complete cycles of viral replication, including the selection of new drug-resistant mutants.