Initiation of therapy during primary HIV type 1 infection results in a continuous decay of proviral DNA and a highly restricted viral evolution

Cure and Long-Term Remission Strategies

The majority of virally suppressed individuals will experience rapid viral rebound upon antiretroviral therapy (ART) interruption, providing a strong rationale for the development of cure strategies. Moreover, despite ART virological control, HIV infection is still associated with chronic immune activation, inflammation, comorbidities, and accelerated aging. These effects are believed to be due, in part, to low-grade persistent transcription and trickling production of viral proteins from the pool of latent proviruses constituting the viral reservoir. In recent years there has been an increasing interest in developing what has been termed a functional cure for HIV. This approach entails the long-term, durable control of viral expression in the absence of therapy, preventing disease progression and transmission, despite the presence of detectable integrated proviruses. One such strategy, the block-and-lock approach for a functional cure, proposes the epigenetic silencing of proviral expression, locking the virus in a profound latent state, from which reactivation is very unlikely. The proof-of-concept for this approach was demonstrated with the use of a specific small molecule targeting HIV transcription. Here we review the principles behind the block-and-lock approach and some of the additional strategies proposed to silence HIV expression.

Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART

The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies.

Here, Bachmann et al. provide data on long-term dynamics of the HIV-1 reservoir in 1,057 individuals on suppressive antiretroviral therapy and show that in 26.6% of individuals the reservoir increases. Viral blips and low-level viremia are significantly associated with a slower reservoir decay.

Re-boost immunizations with the peptide-based therapeutic HIV vaccine, Vacc-4x, restores geometric mean viral load set-point during treatment interruption

Background

Vacc-4x, a therapeutic HIV vaccine candidate has previously induced a significant reduction in viral load (VL) set-point compared to placebo upon interruption of combination anti-retroviral therapy (ART) (2007/1 study). This study, (2012/1), explored the potential to maintain Vacc-4x effect by re-boosting eligible 2007/1 study participants.

Methods

Participant inclusion required 2007/1 participants to have completed all Vacc-4x immunizations and interrupted ART for up to 26 weeks. At weeks (wk)0 and 2, participants received intradermal (i.d.) Vacc-4x booster immunizations (1.2mg) on ART with GM-CSF (60μg) i.d. as a local adjuvant. ART was interrupted for up to 16 weeks (wk12-wk28). Participants were then followed on ART until wk36. VL set-point, total proviral DNA (pvDNA) and immunogenicity assessed by IFN-γ ELISPOT, T-cell proliferation and delayed type hypersensitivity (DTH) reactions were compared to participants’ values in the 2007/1 study where available.

Results

This open, multicenter, clinical study enrolled 33 participants from 9 clinical trial sites in the US and Europe. In the per-protocol (PP) population, the VL set-point geometric mean (GM) 18162 copies/mL was not significantly changed compared to the 2007/1 study (GM VL 22035 copies/mL), (p = 0.453, n = 18). For participants with available preART VL values, the VL set-point (GM 26279 copies/mL) remained significantly lower than the preART VL set-point (GM 74048 copies/mL, p = 0.021, n = 13). A statistically significant reduction in pvDNA (49%) from baseline to wk4 was observed (p = 0.03, n = 26). DTH responses (wk4) increased significantly from baseline (p = 0.006, n = 30) and compared to the 2007/1 study (p = 0.022, n = 29) whilst the proportion of participants with ELISPOT and T-cell proliferation responses was similar between the two studies.

Conclusions

Vacc-4x booster immunizations safely maintained the mean VL set-point at that established following primary Vacc-4x therapeutic immunization. The reduction in pvDNA during ART supports the potential for Vacc-4x immunization to reduce HIV reservoirs and thereby contribute to combination HIV cure strategies.

Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications

HIV-1 DNA persists in infected cells despite combined antiretroviral therapy (cART), forming viral reservoirs. Recent trials of strategies targeting latent HIV reservoirs have rekindled hopes of curing HIV infection, and reliable markers are thus needed to evaluate viral reservoirs. Total HIV DNA quantification is simple, standardized, sensitive, and reproducible. Total HIV DNA load influences the course of the infection and is therefore clinically relevant. In particular, it is predictive of progression to AIDS and death, independently of HIV RNA load and the CD4 cell count. Baseline total HIV DNA load is predictive of the response to cART. It declines during cART but remains quantifiable, at a level that reflects both the history of infection (HIV RNA zenith, CD4 cell count nadir) and treatment efficacy (residual viremia, cumulative viremia, immune restoration, immune cell activation). Total HIV DNA load in blood is also predictive of the presence and severity of some HIV-1-associated end-organ disorders. It can be useful to guide individual treatment, notably, therapeutic de-escalation. Although it does not distinguish between replication-competent and -defective latent viruses, the total HIV DNA load in blood, tissues, and cells provides insights into HIV pathogenesis, probably because all viral forms participate in host cell activation and HIV pathogenesis. Total HIV DNA is thus a biomarker of HIV reservoirs, which can be defined as all infected cells and tissues containing all forms of HIV persistence that participate in pathogenesis. This participation may occur through the production of new virions, creating new cycles of infection and disseminating infected cells; maintenance or amplification of reservoirs by homeostatic cell proliferation; and viral transcription and synthesis of viral proteins without new virion production. These proteins can induce immune activation, thus participating in the vicious circle of HIV pathogenesis.

Are there benefits to starting antiretroviral therapy during primary HIV infection? Conclusions from the Seattle Primary Infection Cohort vary by control group

It is controversial whether starting combination antiretroviral therapy (cART) during primary HIV infection (PHI) is beneficial. Subjects in this observational cohort began cART <30 days (group 1: acute treatment, n = 40), 31-180 days (group 2: early treatment, n = 82) or >180 days (group 3: delayed treatment, n = 35) after HIV infection, and were compared with 27 historical and 60 contemporary controls. Time to HIV-related diagnoses did not differ for group 1 (adjusted hazard ratio [aHR] 1.44, P = 0.3) or group 2 (aHR 1.17, P = 0.5) compared with contemporary controls, but it was delayed for both treated groups (aHR 0.38 for group 1, P = 0.01; and aHR 0.28 for group 2, P < 0.0001) compared with historical controls. Although rates of HIV-related diagnoses were similar in acutely treated subjects and contemporary controls, results were confounded by associations between higher CD4 counts, lower HIV RNA levels and delayed disease progression as reasons for deferring treatment. Randomized trials are needed to address benefits of cART during PHI.

Plasma viral load threshold for sustaining intrahost HIV type 1 evolution

The objective of the present study was to determine if natural suppression of plasma viremia below the detection limit of commercial assays (50-80 copies HIV-1 RNA/ml) can contain the HIV-1 evolution. HIV-1 quasispecies complexity in PBMC DNA was assessed in the env gene at two time points in 14 long-term nonprogressors (LTNPs). Sequence changes consistent with viral evolution was found in all patients with a median plasma RNA viral load >100 copies/ml. Evidence of low-level viral evolution was detected in two of four patients with intermittent viremia and a median plasma HIV-1 RNA load of >80 copies/ml. No significant evolution was observed in the three LTNPs with persistent viral suppression below the detection limit. Overall, a significant positive correlation (p < 0.001) was observed between viral evolution and plasma RNA viral load in the LTNPs analyzed. These results suggest that the detection limit of ultrasensitive viremia assays could represent an important threshold below which intrahost HIV-1 evolution does not occur.

A novel approach to HIV therapy: highly active antiretroviral therapy and autologous hematopoietic cell transplantation

Highly active antiretroviral therapy dramatically decreases in vivo viral replication to levels below the level of clinical detection, but does not eradicate HIV-1 infection on the basis of persistent low-level or cryptic viral replication and latent provirus in resting CD4+ T lymphocytes. Immune activation therapy has begun to be used in attempts to increase the turnover rate of the latent virus reservoir through activation of infected cells that comprise this reservoir, in order to promote cell death and accelerate virus clearance. Recent reports have not demonstrated complete virus ablation. Autologous hematopoietic cell transplantation now appears as a safe, feasible, and reasonable approach for Aids-related lymphoma in patients who meet criteria for transplantation. The hypothesis is based on the possibility that hematopoietic stem cells from a HIV-positive patient could be collected before the patient becomes infected with HIV. Then, the proposed treatment consists of the following assumptions. HAART keeps viral replication below the level of detection, limiting the infection to latent provirus in resting CD4+ T lymphocytes. It is presumed here that myeloablative conditioning regimen can lead to the killing of all the cells that, in theory, harbour the virus. The following transplantation of the autologous hematopoietic stem cells, collected before HIV infection, would allow the complete recovery. The hypothesis is to be tested on a suitable animal model. After the collection of hematopoietic stem cells, the animal is experimentally infected with the immunodeficiency virus. HAART is given after plasma viral RNA becomes detectable. By myeloablative conditioning regimen all the cells harbouring the virus are supposed to be killed. Then, as the viral load is kept undetectable by HAART, the animal undergoes autologous hematopoietic stem cell transplantation. Antiretroviral therapy is interrupted a month after engraftment has taken place. Although hematopoietic stem cells from man before infection with HIV are unlikely to be available, a successful test on the animal would suggest a new approach which could allow the cure of HIV in future.

The role of hydroxyurea in enhancing the virologic control achieved through structured treatment interruption in primary HIV infection: final results from a randomized clinical trial (Pulse)

BACKGROUND

Structured treatment interruptions (STIs) have been postulated to improve virologic control in primary HIV infection (PHI) by stimulating HIV-specific T-lymphocyte immunity. The addition of hydroxyurea (HU) may reduce viral production from activated CD4 cells.

METHODS

Patients with PHI received a standardized antiretroviral (ARV) regimen consisting of indinavir 800 mg twice daily (BID), ritonavir 100 mg BID, didanosine 400 mg (QD), and either stavudine 40 mg BID or lamivudine 150 mg BID, for up to 12 months and were randomized to HU 500 mg BID or not. If viral suppression (<50 copies/mL) was achieved, up to 3 STIs were undertaken. Two ARV cycles were allowed after each interruption if virologic rebound to more than 5000 RNA copies/mL occurred. Treatment success was defined as maintaining viral loads below 5000 copies/mL for 6 months after ARV interruption.

RESULTS

Sixty-eight male homosexual patients were randomized: 35 to ARV + HU and 33 to ARV-alone. Median baseline HIV RNA was 5.73 log10 copies/mL, and median CD4 T-lymphocyte count was 517 cells/microL. Treatment success was not significantly different between those receiving and not receiving HU, with 9 (26%) and 9 (27%), respectively, maintaining viral load at less than 5000 copies/mL in each group (P = 0.88). Virologic control was achieved by 11 (19%) of 59 after 1 STI, 1 (2%) of 41 after 2 STIs, and 6 (17%) of 36 after the third STI. Serious adverse events were recorded for 9 (26%) of 35 of patients using HU and 3 (9%) of 33 in the ARV-only group (P = 0.28). CD4 cell increases were significantly blunted for the HU group compared to the ARV-alone group after the initial treatment phase (+101 cells vs. +196 cells, respectively, P = 0.006).

CONCLUSIONS

Hydroxyurea was not found to be beneficial when used in association with STIs in patients during PHI.

Nucleotide and amino acid mutations in human immunodeficiency virus corresponding to CD4+ decline

In a meta-analysis, gene sequences of the HIV-1 V3 and surrounding envelope region from studies examining longitudinally derived blood and plasma human immunodeficiency virus forms were analyzed for changes over disease course. CD4+ counts were used as a marker of disease progression; 58 subjects, followed an average of 56 months, were included. Genetic diversification was found early in disease progression. In mid-progression (CD4+ counts dropping from 488 to 329/mm3) diversification did not increase while loop charge dramatically increased. This is consistent with a charged form that dominates and induces disease progression at this critical time. Although the overall mean increase in loop charge was significant, this increase and the transition to amino acids known to change tropism occurred in only half of the subjects who progressed. Those with rapidly progressing disease (within 2 years post-infection) began with a loop charge similar to the end stage of normal progressors. DNA from blood-cell-derived sequences differed from concurrently obtained plasma counterparts by one nucleotide out of 238, but this difference was not reflected in differences in glycosylation patterns, loop charge, or tropism-conferring amino acids. Plasma-derived forms were poorer predictors of future viral forms than were cell-derived sequences.

Primary HIV Infection

Primary HIV infection refers to the events surrounding acquisition of HIV infection. It is associated with a nonspecific clinical syndrome that occurs 2 to 4 weeks after exposure in 40% to 90% of individuals acquiring HIV. Patients identified before seroconversion often have very high plasma HIV RNA titers that, without treatment, gradually decrease to reach a set point. Treatment of primary HIV infection with highly active antiretroviral therapy does not prevent establishment of chronic infection. However, very early therapy could potentially decrease the viral set point, prevent viral diversification, preserve immune function, improve clinical outcomes, and decrease secondary transmission. These benefits have not yet been definitely demonstrated. Transmission of viral strains with decreased susceptibility to antiviral drugs has led to recommendations for resistance testing in primary infection before initiation of therapy. Immunomodulators and vaccines are also under study as adjuvant therapy for treatment of primary HIV infection.

Changes in the human immunodeficiency virus V3 region that correspond with disease progression: a meta-analysis

In order to determine the changes in the human immunodeficiency virus type-1 (HIV-1) envelope that corresponds with disease progression, a meta-analysis of viral forms was performed using HIV-1 sequences obtained from GenBank. Studies were selected that included longitudinally derived V3 envelope region sequences from multiple time points along with CD4 values as a marker of disease progression. Studies with a total of 58 subjects, 327 time points, and 380,000 total amino acid residues were included in this meta-analysis. Changes at specific amino acid sites over the course of disease progression stages were analyzed. The most common specific changes were found at amino acid sites 324D to N, 306S/G to R, and 360N to R. Other sites had changes from one amino acid type to another including the appearance of a basic form at 327, a charged form at 319, and 320D/E changing to basic or neutral. The timing of these changes was contrasted to CD4 decline with changes at 324 and 327 appearing before and 306, 320, and 319 appearing after the initiation of CD4 decline.

HIV type 1 DNA development during long-term supervised therapy interruption

We studied the pattern of HIV-1 DNA development and the association to other HIV-related factors during long-term supervised therapy interruption (LT-STI). Fifteen patients were treated with long-time protease inhibitor-based antiretroviral therapy (PI-ART). They had HIV-1 RNA at <50 copies/ml over 33.4 (SD 9.5) months and CD4(+) cell counts of 875 (SD 415) x 10(6)/liter. A real-time polymerase chain reaction, amplifying fragments of the HIV-1 pol gene and the human albumin gene simultaneously, was used to quantify HIV-1 DNA molecules in CD4(+) cells. The quantity of HIV-1 DNA in CD4(+) cells increased during LT-STI in all 15 patients, with an average doubling time of 2 months. Tentatively, three patterns were observed: rapid initial increase with subsequent stabilizing levels, rapid continuous increase, and slow increase. The HIV-1 DNA slope was positively related to the HIV-1 RNA maximum and steady state level and the baseline HIV-1 DNA value. It was inversely related to the decrease in CD4(+) cells both before the start of PI-ART and during the LT-STI. To conclude, HIV-1 DNA persists in infected CD4(+) cells despite long-term effective PI-ART and will increase after therapy interruption. The most important clinical predictor of long-term STI failure was the rapid CD4(+) cell decline before PI-ART. In patients with a steep pre-PI-ART slope it may be prudent to continue treatment and not initiate therapy interruption.

Follow-up of antiretroviral treatment in liver transplant recipients with primary and chronic HIV type 1 infection

The prognosis of HIV-1-infected patients has dramatically improved but progression to liver failure occurs now frequently in subjects coinfected with hepatitis C virus (HCV). This has raised the issue of organ transplantation, but the knowledge about the effect of concomitant antiretroviral and immunosuppressive therapy is limited. The objective of the study was to describe viral and immunological events in antiretroviral-treated orthotopic liver transplant (OLT) recipients with primary (PHI) or chronic HIV-1 infection. Three HIV-1-infected patients with liver cirrhosis due to chronic HCV infection underwent OLT. A fourth patient developed PHI at OLT. Immunosuppressive drugs and combination antiretroviral therapy were given. The effects on HIV-1 load, viral diversity and divergence, and CD4(+) T cell counts, were studied. One patient died after 3 months. Three subjects were alive after 9 months, 14 months, and 3 years, respectively. In the PHI patient, viral load decreased during the second week of illness despite immunosuppression. During the third week the viremia increased until antiretroviral treatment was initiated. In all four patients, the HIV-1 replication was effectively inhibited during follow-up by the treatment, as determined by undetectable plasma viremia, lack of viral sequence changes, and increase in CD4(+) T cells. The pattern of viral dynamics may suggest that the innate immunity causes the earliest decline of viral load in PHI patients. A lack of adaptive immunity may thereafter lead to an increase in viremia in heavily immunosuppressed individuals. However, a specific HIV-1 immunity is not necessary to efficiently inhibit the viral replication when potent antiretroviral therapy is given in liver transplant recipients with primary or chronic HIV-1 infection.

Approaching eradication of highly active antiretroviral therapy-persistent human immunodeficiency virus type 1 reservoirs with immune activation therapy

Highly active antiretroviral therapy (HAART) has dramatically altered the human immunodeficiency virus type 1 (HIV-1) pandemic in the developed world. Most patients treated with HAART will maintain clinically undetectable plasma virus loads with concomitant dramatic decreases in mortality and morbidity. Nevertheless, HAART does not eradicate HIV-1 infection on the basis of persistent low-level or cryptic viral replication and, of importance, latent provirus in resting CD4+ T lymphocytes. New approaches are now being developed for stimulation of "HAART-persistent" reservoirs. Immune activation therapy (IAT) has begun to be used in attempts to stimulate the HIV-1 latent reservoir. These studies and new approaches to activating latent virus in resting CD4+ T cells are reviewed and critically analyzed in the present report. Development of novel IAT may lead to long-term remission or viral eradication in the future.

Slowly declining levels of viral RNA and DNA in DNA/recombinant modified vaccinia virus Ankara-vaccinated macaques with controlled simian-human immunodeficiency virus SHIV-89.6P challenges

In a recent vaccine trial, we showed efficient control of a virulent simian-human immunodeficiency virus SHIV-89.6P challenge by priming with a Gag-Pol-Env-expressing DNA and boosting with a Gag-Pol-Env- expressing recombinant-modified vaccinia virus Ankara. Here we show that long-term control has been associated with slowly declining levels of viral RNA and DNA. In the vaccinated animals both viral DNA and RNA underwent an initial rapid decay, which was followed by a lower decay rate. Between 12 and 70 weeks postchallenge, the low decay rates have had half-lives of about 20 weeks for viral RNA in plasma and viral DNA in peripheral blood mononuclear cells and lymph nodes. In vaccinated animals the viral DNA has been mostly unintegrated and has appeared to be largely nonfunctional as evidenced by a poor ability to recover infectious virus in cocultivation assays, even after CD8 depletion. In contrast, in control animals, which have died, viral DNA was mostly integrated and a larger proportion appeared to be functional as evidenced by the recovery of infectious virus. Thus, to date, control of the challenge infection has appeared to improve with time, with the decay rates for viral DNA being at the lower end of values reported for patients on highly active antiretroviral therapy.

The selection and evolution of viral quasispecies in HIV-1 infected children

OBJECTIVES

To analyse the diversity and divergence of the viral populations in three mother-child pairs in longitudinally obtained samples for up to 7 years.

METHODS

Peripheral blood mononuclear cells were obtained from three mothers at delivery and three to four samples were obtained from each of their children from 1.5 months up to 78 months of age. The V3 region of HIV-1 was amplified by polymerase chain reaction, cloned and sequenced. HIV-1 DNA sequence comparisons were performed by phylogenetic analysis.

RESULTS

The viral population was initially homogenous in two children but highly heterogeneous in one child. Three patterns of vertical transmission seemed to have occurred: transmission of the most prevalent maternal strain, of a minor maternal strain and of multiple maternal strains. In one child, a possible reappearance of a maternal sequence was observed at 34 months of age.

CONCLUSIONS

Children may become infected with the most prevalent maternal strain, a minor maternal variant or multiple maternal quasispecies. Maternal viral variants may reappear in children after several years of infection and could possibly be derived from a reservoir of founder quasispecies established during the children's primary HIV-1 infection.