Mechanisms of HIV-1 persistence in the presence of highly active antiretroviral therapy (HAART)

In HIV-1-infected patients well suppressed on highly active antiretroviral therapy (HAART), a low level of residual plasma virus exists below the limit of detection for most standard clinical assays. However, it is not yet clear whether this plasma virus reflects release of virus from the latent reservoir or ongoing replication that could allow emergence of drug resistance. In order to understand the nature of this low level viremia, there is an urgent need for an assay that can detect new cycles of infection in patients receiving HAART who have plasma HIV-1 RNA levels below the limit of detection.; One possible method relies on identifying a marker of recently infected cells, such as labile DNA intermediates in the HIV lifecycle. We evaluated the utility of circular forms (2LTR circles) of the viral genome as potential markers. Our in vitro analyses of the decay of these circles reveal that they are highly stable and decay only due to dilution by cell division. Therefore, the utility of 2-LTR circles in the study of viral dynamics is limited.; Alternatively, if more sensitive assays could be developed that allow genotypic analysis of this low level virus, it may be possible to determine whether viral evolution is occurring through the detection of drug resistant mutations emerging during low levels of replication in the presence of antiretroviral drugs. We describe a longitudinal, clonal genotypic analysis of plasma virus in 8 treated adults who had suppression of viremia to undetectable levels for up to 15 months. Using analytical approaches for distinguishing selected resistance mutations from nonselected mutations and polymerase chain reaction errors, we detected no evolution of resistance in the reverse-transcriptase and protease genes. Thus, in some patients, HAART suppresses replication to a level that does not allow the evolution of drug resistance over a time frame of years.; Many patients suppressed on HAART experience intermittent episodes of detectable low-level viremia (blips). Blip dynamics and their potential role as a cause or result of developing drug resistance have been imprecisely defined. We obtained frequent viral load measurements and genotypes of 10 well suppressed patients on HAART. Blips were generally not concordant on independent testing, were short in duration (<3 days), low in magnitude (<100 c/ml), and not association with the development of new genotypic resistance mutations. In conclusion, most blips represent normal biological and statistical variation around mean levels that are below 50 copies/ml rather than clinically significant elevations in viral replication.; Finally, we generated an extensive compilation of sequences from the low level plasma virus persisting in these patients suppressed on HAART in order to compare them to sequences found in the resting cells of the latent reservoir. Phylogenetic and genotypic analyses of sequences obtained from both compartments provided unexpected insights into the nature of this low level persistent viremia.