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Latency and viral persistence in HIV-1 infection

Janet D. Siliciano and Robert F. Siliciano

Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

Address correspondence to: Robert F. Siliciano, Department of Medicine, Johns Hopkins University School of Medicine, 1049 Ross Building, 720 Rutland Avenue, Baltimore, Maryland 21205, USA. Phone: (410) 955-2958; Fax: (410) 955-0964; E-mail:

Published October 1, 2000

HIV-1 infection can be controlled with combinations of antiretroviral drugs, an approach known as highly active antiretroviral therapy (HAART). In patients who respond well to HAART, viremia decreases to below the limits of detection, disease progression stops, and reconstitution of the immune system begins. For the first time since the beginning of the epidemic, the possibility of curing HIV-1 infection has been seriously considered (1). However, optimism regarding the eradication of HIV-1 infection is tempered by the appreciation that a latent reservoir for HIV-1 exists in resting memory CD4+ T cells (2, 3) and persists in patients on HAART (46). Hence a rebound in viremia seems inevitable if therapy is stopped, a prediction borne out in recent studies. The source of this rebound virus has not been determined. An important study by David Ho and colleagues in this issue of JCI (7) suggests that the latent reservoir may be the source of this rebound virus.

The formation of the latent reservoir for HIV-1 is best understood in the context of the normal T-cell physiology. HIV-1 replicates well in activated CD4+ T cells. Most of these infected lymphoblasts die quickly (t1/2 = 1 day), due to viral cytopathic effects and/or host immune mechanisms (8, 9). A small fraction of infected lymphoblasts survive and revert back to a resting state by the same process that normally generates memory T cells. However, in this case the memory cells harbor an integrated copy of the HIV-1 genome. Although these cells do not continue to produce virus while in a resting state, they can function as a latent reservoir, capable of reinitiating virus production upon reactivation. This reservoir is extremely stable due to the fundamental biology of memory cells, which must survive for many years to provide protection against previously encountered antigens. The observed decay rate of latently infected resting CD4+ cells is extremely slow in most patients on HAART, with a half-life of 44 months in the typical patient (10). Based on an estimate of 106 cells in the latent reservoir (3), 73 years of therapy would be required for eradication.

To determine whether this latent reservoir is a source of the rebound viruses that appear following interruption of HAART, Zhang et al. (7) examined variable regions of the HIV-1 envelope (env) genes of rebounding viruses in eight patients who went off of effective HAART regimens. Using a PCR assay for length polymorphisms in variable regions of env, the authors compared sequences from rebounding viruses with those from viruses isolated from resting CD4+ T cells during treatment. In five patients, env sequences from rebound viruses were identical in length to sequences in the latent reservoir. The authors conclude that in this subset of patients, the rebound virus was likely derived from latently infected CD4+ T cells. However, env sequences amplified from initial rebound viruses from the other three patients were different in length from latent reservoir sequences. Two of these patients also had evidence of ongoing virus production on HAART. Using a different approach, Chun et al. have also observed similarities between the rebound virus and viruses in the latent reservoir in some but not all patients (11). These authors have interpreted their results differently, focusing on the idea that HIV-1 may persist not only in the latent reservoir but in additional as-yet undefined sites as well.

Caveats and questions

Both of these studies provide insights into mechanisms of viral persistence. There are caveats, however, related to sampling and founder effects. Individual viral variants that are released from a reservoir at the time HAART is stopped will have a chance to expand unhindered by antiretroviral drugs. The rebound virus may therefore be derived from a small number of cells in the reservoir that happened to be activated when HAART was stopped. If the viral repertoire is diverse, this rebound virus represents only a small sample of the reservoir and may or may not match samples obtained directly from the reservoir depending on the degree of viral diversity and the number of samples analyzed. Therefore, observed differences between the latent reservoir virus and the rebound virus may simply result from insufficient sampling and cannot be used to say definitively that the rebound virus came from a particular location. Sampling is less of a concern in the study of Zhang et al. (7), due to the fact that the patients studied were all started on HAART within 90 days of infection, conditions that limit viral diversity. The simplest interpretation of both studies is that, in many cases, viruses in the latent reservoir resemble the rebound virus; where differences exist, they may reflect sampling problems, the presence of additional long-term reservoirs for HIV-1, or the failure of HAART to completely halt viral replication.

Zhang et al. (7) go on to suggest that in the patients who have the best suppression of viral replication on HAART, the latent reservoir and rebound viruses will be genetically matched, but that in patients who have evidence of incomplete suppression, the rebound virus will derive from a population that has continued to replicate at low levels and will be distinct from the latent reservoir. Recent studies have indeed documented the inability of the HAART regimens to completely suppress virus production (1214). Of course, continued low-level virus production could reflect release of virus from some stable reservoir without the generation of newly infected cells. However, the detection of labile replicative intermediates (13, 15) or temporal sequence evolution (12, 16) suggests that new cycles of infection may occur even in patients who have responded well to HAART.

The kinetics of viral rebounding

How is ongoing viral replication related to the persistence of HIV-1 in the latent reservoir and to the rebound virus seen after cessation of HAART? Figure 1 illustrates viral decay curves under several different conditions. In the hypothetical absence of viral reservoirs and residual replication on HAART, eradication would be possible due to the fact that the infected CD4+ T lymphoblasts and macrophages that produce most of the plasma virus have relatively short half-lives (1 day and 2 weeks, respectively), giving rise to the classic biphasic decay curve originally defined by Ho and colleagues (1). The second, slower phase of decay is still fast enough to allow eradication of residual infected cells in 2–3 years. However, since it is now clear that the virus persists in a stable reservoir in resting CD4+ T cells, some residual virus production must continue in most patients on HAART. These two phenomena are related in that the extraordinary stability of the latent reservoir in most patients on HAART (t1/2 = 44 months) (10) may be due in part to replenishment of the reservoir by low-level ongoing viral replication. It is also likely that release of virus from the latent reservoir contributes to the low-level ongoing replication observed in most patients. If HAART is interrupted, viruses that are actively replicating will expand quickly, producing a rebound of viremia to high levels in about 2 weeks. In the hypothetical case of HAART regimens that completely prevent new infection of susceptible cells, a rebound would nevertheless occur, due to activation of latently infected cells.

Hypothetical decay curves showing plasma virus levels in patients starting Figure 1

Hypothetical decay curves showing plasma virus levels in patients starting and stopping HAART. (a) Biphasic decay curve of plasma HIV-1 RNA levels following initiation of HAART (1). Values below the limit of detection (20 copies/ml) are extrapolated and/or hypothetical. If HAART completely stopped ongoing viral replication, and if there were no stable reservoirs, eradication would be possible since the second phase of decay extrapolates to <1 residual infected cell in 2–3 years. (b) Decay curve showing additional effect of the latent reservoir in resting CD4+ T cells. If HAART stopped all residual viral replication, plasma viremia would decrease to the point where the only virus entering the plasma would be that derived from the occasional activation of latently infected resting CD4+ T cells. The decay rate of this latent reservoir is slow, with a half-life of at least 6 months in patients who have optimal suppression of viral replication on HAART (12, 17) and as long as 44 months in most patients on HAART (10). (c) Viral decay curve expected in most patients on HAART. Virus production continues at a level below the limit of detection of current ultrasensitive assays. Many patients have occasional “blips” of viremia that reach into the detectable range. In these patients, the latent reservoir persists with an extremely long half-life (44 months). (d) Effect of treatment interruption. A rapid rebound is expected due to the fact that most patients have continued virus production while on HAART. Viruses that are produced at the time HAART is stopped will replicate rapidly. (e) Effect of treatment interruption in patients who have no residual viral replication on HAART. A rebound is still expected due to activation of cells in the latent reservoir.

Viewed in this context, several research goals assume paramount importance. First, it is critical to determine whether additional viral reservoirs exist. Second, it is important to understand the nature and source of the ongoing virus production that is seen in most patients on HAART. Finally, novel approaches are needed to eliminate latently infected cells, which clearly represent a very serious barrier to HIV-1 eradication.


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