Episomal viral cDNAs identify a reservoir that fuels viral rebound after treatment interruption and that contributes to treatment failure

Viral reservoirs that persist in HIV-1 infected individuals on antiretroviral therapy (ART) are the major obstacle to viral eradication. The identification and definition of viral reservoirs in patients on ART is needed in order to understand viral persistence and achieve the goal of viral eradication. We examined whether analysis of episomal HIV-1 genomes provided the means to characterize virus that persists during ART and whether it could reveal the virus that contributes to treatment failure in patients on ART. For six individuals in which virus replication was highly suppressed for at least 20 months, proviral and episomal genomes present just prior to rebound were phylogenetically compared to RNA genomes of rebounding virus after therapy interruption. Episomal envelope sequences, but not proviral envelope sequences, were highly similar to sequences in rebounding virus. Since episomes are products of recent infections, the phylogenetic relationships support the conclusion that viral rebound originated from a cryptic viral reservoir. To evaluate whether the reservoir revealed by episomal sequence analysis was of clinical relevance, we examined whether episomal sequences define a viral population that contributes to virologic failure in individuals receiving the CCR5 antagonist, Vicriviroc. Episomal envelope sequences at or near baseline predicted treatment failure due to the presence of X4 or D/M (dual/mixed) viral variants. In patients that did not harbor X4 or D/M viruses, the basis for Vicriviroc treatment failure was indeterminate. Although these samples were obtained from viremic patients, the assay would be applicable to a large percentage of aviremic patients, based on previous studies. Summarily, the results support the use of episomal HIV-1 as an additional or alternative approach to traditional assays to characterize virus that is maintained during long-term, suppressive ART.

Infection by HIV-1 and the related effects on human health continue to be a major problem throughout the world. Since the early 1980's, more than 25 million people have died from AIDS and the only treatment option for infected individuals is likely to be life-long treatment with a combination of antiviral drugs. While antiviral drug therapy can reduce viral replication to levels that are undetectable by currently used assays, there is a rapid recrudescence of viremia upon interruption of therapy. This indicates that there are viral reservoirs, undetectable by conventional diagnostic assays that sustain the virus in the face of ART. We have developed an alternative or additional approach to study cryptic viral replication based on episomal HIV-1 genomes. Although HIV-1 episomes are not suitable substrates for integration and thus are dead-end products in the viral life cycle, episomal HIV-1 genomes are useful surrogate markers of viral replication since they are labile and indicative of recent infection events. Here we have used episomal HIV-1 analysis to study the reservoir that fuels viral rebound during treatment interruption and to demonstrate the utility of this approach in guiding the clinical treatment of infected individuals.