Abstract
Combination antiretroviral therapy controls but does not cure HIV-1 infection because a small fraction of cells harbor latent viruses that can produce rebound viremia when therapy is interrupted. The circulating latent virus reservoir has been documented by a variety of methods, most prominently by viral outgrowth assays (VOAs) in which CD4+ T cells are activated to produce virus in vitro, or more recently by amplifying proviral near full-length (NFL) sequences from DNA. Analysis of samples obtained in clinical studies in which individuals underwent analytical treatment interruption (ATI), showed little if any overlap between circulating latent viruses obtained from outgrowth cultures and rebound viruses from plasma. To determine whether intact proviruses amplified from DNA are more closely related to rebound viruses than those obtained from VOAs, we assayed 12 individuals who underwent ATI after infusion of a combination of two monoclonal anti-HIV-1 antibodies. A total of 435 intact proviruses obtained by NFL sequencing were compared with 650 latent viruses from VOAs and 246 plasma rebound viruses. Although, intact NFL and outgrowth culture sequences showed similar levels of stability and diversity with 39% overlap, the size of the reservoir estimated from NFL sequencing was larger than and did not correlate with VOAs. Finally, intact proviruses documented by NFL sequencing showed no sequence overlap with rebound viruses; however, they appear to contribute to recombinant viruses found in plasma during rebound.
Highlights
Combination antiretroviral therapy controls but does not cure HIV1 infection because a small fraction of cells harbor latent viruses that can produce rebound viremia when therapy is interrupted
near full-length (NFL) proviral genomes were amplified from DNA extracted from purified CD4+ T cells obtained from the two leukapheresis samples from nine individuals that maintained viral suppression for >12 wk after analytical treatment interruption (ATI), including two that remained virologically suppressed during the entire observation period (>30 wk, participants 9254 and 9255) [11, 17, 20]
3SEQ recombination algorithm, we found that 48% of the rebound viruses could be recombinants between intact NFL and/or Q2VOA proviruses
Summary
Combination antiretroviral therapy controls but does not cure HIV1 infection because a small fraction of cells harbor latent viruses that can produce rebound viremia when therapy is interrupted. The circulating latent virus reservoir has been documented by a variety of methods, most prominently by viral outgrowth assays (VOAs) in which CD4+ T cells are activated to produce virus in vitro, or more recently by amplifying proviral near full-length (NFL) sequences from DNA. Numerous methods have been evaluated to measure the latent reservoir, viral outgrowth assays (VOAs) are considered to be the gold standard [2, 4] In this assay, infected donor CD4+ T cells are activated in vitro to induce HIV-1 production in the presence of uninfected recipient CD4+ T cells. There are several caveats to interpreting the results of the VOAs: (i) The assay is highly variable and any difference of less than sixfold is not considered to be significant [10]; (ii) a single round of stimulation captures only a fraction of the latent cells that can be reactivated [6]; (iii) individual latent cells differ in their requirements for reactivation [11]; (iv) VOAs are typically performed on cells derived from blood and this compartment may not be representative of the entire latent reservoir [12]; and (v) the requirements for reactivation in vitro and in vivo may differ significantly [13, 14]
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