MicrobiologyBytes

When HIV infects a T lymphocyte, it first inserts a copy of its genome into the cell’s DNA. This inserted virus, called a provirus, then races to make as many new viruses as possible before its host cell dies. But in a few infected cells, HIV does not immediately turn its host into a viral factory. Instead, the provirus is carried around in the DNA of the cell as a transcriptionally silent (“latent”) passenger, only to explode back into action at a later time, when its host cell attempts to participate in an immune response to infection by other pathogens. Because they target the products of HIV transcription, current antiviral therapies like HAART can’t kill latent HIV. And because a full-blown infection can be re-established from a tiny reservoir of latently infected cells, viral latency is an important contributor to our struggle against HIV (Dissecting HIV’s Latent Menace. (2011) PLoS Biol 9(11): e1001209).

The following article examines the molecular mechanism responsible for the establishment and maintenance of HIV latency and its re-activation, and uncovers the role played in this process by the SWI/SNF class of chromatin remodeling complexes, which use energy from ATP to alter the structure of chromatin. Two distinct sub-classes of SWI/SNF, BAF and PBAF, play functionally opposing roles in distinct steps of the HIV promoter (or long terminal repeat, LTR) transcription cycle. The PBAF complex augments transcription of the LTR by the viral transactivator Tat. In contrast, the distinct BAF complex generates a chromatin structure at the LTR that is energetically unfavorable with respect to the intrinsic histone-DNA sequence preferences. Specifically, BAF positions a repressive nucleosome immediately downstream of the HIV transcription start site, abrogating transcription, and in this way contributes to the establishment and maintenance of HIV latency. The data describe a novel molecular mechanism for the establishment and maintenance of HIV latency, and we identify the catalytic subunit of BAF, the enzyme BRG1, as a putative molecular target to deplete the latent reservoir in infected patients.

Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency. (2011) PLoS Biol 9(11): e1001206
Persistence of a reservoir of latently infected memory T cells provides a barrier to HIV eradication in treated patients. Several reports have implicated the involvement of SWI/SNF chromatin remodeling complexes in restricting early steps in HIV infection, in coupling the processes of integration and remodeling, and in promoter/LTR transcription activation and repression. However, the mechanism behind the seemingly contradictory involvement of SWI/SNF in the HIV life cycle remains unclear. Here we addressed the role of SWI/SNF in regulation of the latent HIV LTR before and after transcriptional activation. We determined the predicted nucleosome affinity of the LTR sequence and found a striking reverse correlation when compared to the strictly positioned in vivo LTR nucleosomal structure; sequences encompassing the DNase hypersensitive regions displayed the highest nucleosome affinity, while the strictly positioned nucleosomes displayed lower affinity for nucleosome formation. To examine the mechanism behind this reverse correlation, we used a combinatorial approach to determine DNA accessibility, histone occupancy, and the unique recruitment and requirement of BAF and PBAF, two functionally distinct subclasses of SWI/SNF at the LTR of HIV-infected cells before and after activation. We find that establishment and maintenance of HIV latency requires BAF, which removes a preferred nucleosome from DHS1 to position the repressive nucleosome-1 over energetically sub-optimal sequences. Depletion of BAF resulted in de-repression of HIV latency concomitant with a dramatic alteration in the LTR nucleosome profile as determined by high resolution MNase nucleosomal mapping. Upon activation, BAF was lost from the HIV promoter, while PBAF was selectively recruited by acetylated Tat to facilitate LTR transcription. Thus BAF and PBAF, recruited during different stages of the HIV life cycle, display opposing function on the HIV promoter. Our data point to the ATP-dependent BRG1 component of BAF as a putative therapeutic target to deplete the latent reservoir in patients.

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A new study has confirmed the existence of a “trial effect” in clinical trials for treatment of HIV. Trial effect is an umbrella term for the benefit experienced by study participants simply by virtue of their participating in the trial. It includes the benefit of newer and more effective treatments, the way those treatments are delivered, increased care and follow-up, and the patient’s own behavior change as a result of being under observation.

Researchers compared HIV suppression among patients who began highly active antiretroviral therapy (HAART) in a clinical trial with patients who received HAART in routine clinical care in two different time periods, 1996-1999 and 2000-2006. They found clear evidence of a trial effect during the earlier period, but not during the later period. Researchers offer that improvements to antiretroviral therapy (fewer pills and fewer side effects), and the change in attitude to HIV, which has come to be seen by many as a chronic, but treatable infection, may be among the explanations for the lack of demonstrable trial effect in the later period.

This is the first study to clearly demonstrate a trial effect in HIV clinical trials, and this has important implications moving forward. Documentation of a clinical trial effect should be considered when interpreting the generalizability of clinical trial results. At the same time, the fact that no trial effect was observed in the current HAART period argues that the efficacy demonstrated in clinical trials is likely to predict the effectiveness of the therapy in broader treatment populations. Clinicians and public health officials may have increased confidence that treatment guidelines based on clinical trial data are relevant to routine clinical care.

Does HAART Efficacy Translate to Effectiveness? Evidence for a Trial Effect. PLoS ONE 6(7): e21824. doi:10.1371/journal.pone.0021824
Background: Patients who participate in clinical trials may experience better clinical outcomes than patients who initiate similar therapy within clinical care (trial effect), but no published studies have evaluated a trial effect in HIV clinical trials.
Methods: To examine a trial effect we compared virologic suppression (VS) among patients who initiated HAART in a clinical trial versus in routine clinical care. VS was defined as a plasma HIV RNA #400 copies/ml at six months after HAART initiation and was assessed within strata of early (1996–99) or current (2000–06) HAART periods. Risk ratios (RR) were estimated using binomial models.
Results: Of 738 persons initiating HAART, 30.6% were women, 61.7% were black, 30% initiated therapy in a clinical trial and 67% (n = 496) had an evaluable six month HIV RNA result. HAART regimens differed between the early and current periods (p,0.001); unboosted PI regimens (55.6%) were more common in the early and NNRTI regimens (46.4%) were more common in the current period. Overall, 78% (95%CI 74, 82%) of patients achieved VS and trial participants were 16% more likely to achieve VS (unadjusted RR 1.16, 95%CI 1.06, 1.27). Comparing trial to non-trial participants, VS differed by study period. In the early period, trial participants initiating HAART were significantly more likely to achieve VS than non-trial participants (adjusted RR 1.33; 95%CI 1.15, 1.54), but not in the current period (adjusted RR 0.98; 95%CI 0.87, 1.11).
Conclusions: A clear clinical trial effect on suppression of HIV replication was observed in the early HAART period but not in the current period.

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The main impediment to a cure for HIV is the existence of long-lasting treatment resistant virus reservoirs. This review discusses what is currently known about reservoirs, including their formation and maintenance, while focusing on latently infected CD4+ T cells. It compares several different in vivo and in vitro models of latency and comments on how each model may reflect the properties of reservoirs in vivo, especially with regard to cell phenotype, since recent studies demonstrate that multiple CD4+ T cell subsets contribute to HIV reservoirs and that with HAART and disease progression the relative contribution of different subsets may change. It also focuses on the direct infection of resting CD4+ T cells as a source of reservoir formation and as a model of latency, since recent results help explain the misconception that resting CD4+ T cells appeared to be resistant to HIV in vitro.

HIV reservoirs and latency models. Virology. 2011 411(2): 344-354

On June 5 1981, MMWR published a report of Pneumocystis carinii pneumonia in five previously healthy young men in Los Angeles, California; two had died. This report later was acknowledged as the first published scientific account of what would become known as human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS). Thirty years after that first report, the most recent estimate is that 33.3 million persons were living with HIV infection worldwide at the end of 2009.

In 1981 I was working on my PhD (on poliovirus) when I first heard about AIDS. Someone from the department came back from a trip to San Francisco with lurid and scary tales. Over the next couple of years, my interest in retroviruses grew and when I finished my PhD in 1984, I went off to California to work on HTLV and HIV.

In the United States, CDC estimates that 1,178,350 persons were living with HIV at the end of 2008, with 594,496 having died from AIDS since 1981. At this 30-year mark, efforts are being accelerated under the National HIV/AIDS Strategy of the United States, with goals of reducing the number of persons who become infected with HIV, increasing access to care and optimizing health outcomes for persons living with HIV, and reducing HIV-related health disparities.

I worked on HIV for 10 years before moving on to other things. I still maintain a close interest in the topic. 30 years – it seems like yesterday.

MMWR 60(21): 689 June 3 2011

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“A new vaccine can protect macaques against the monkey equivalent of HIV and could provide a fresh approach to an HIV vaccine, a study suggests. US researchers say the vaccine offered protection to 13 of 24 rhesus macaques treated in the experiment. In 12 of the monkeys, the vaccine was still effective 12 months later.”

via BBC News – Monkey HIV vaccine ‘effective’, say researchers

MicrobiologyBytes: Encouraging news but – 50% protection against the same strain of virus after 12 months? Would you trust your life to this?

Original Source: Profound early control of highly pathogenic SIV by an effector memory T-cell vaccine. Nature 11 May 2011 doi:10.1038/nature10003 (subscription required)

It is commonly accepted that the spread of most viruses occurs via the diffusion of ‘cell-free’ viral particles. In support of this, infectious viruses have been found in biological fluids and aerosols, and could be propagated in vitro using virus stocks produced from infected cell-culture supernatants. This mode of viral dissemination requires high numbers of stable viral particles released by the infected cell into the extracellular environment, such as the host bodily fluids. ‘Free’ viral particles were associated with a variety of components, such as lipids or proteins, which might reinforce virus envelop integrity and prevent envelope glycoprotein shedding. However, for other viruses, few viral particles are released, or they are poorly infectious when separated from infected cells. In such cases, virus propagation largely requires the presence of infected cells, suggesting that cell contacts mediate viral spread. This type of dissemination is mainly reported for enveloped viruses, such as some herpes viruses and some retroviruses, particularly deltaretroviruses such as the human T-cell leukemia virus type 1 (HTLV-1). Many aspects of this mode of virus dissemination are largely unknown, such as (i) the nature and the mechanism for forming cellular junctions that mediate cell–cell virus spread, and (ii) the nature of the infectious material transferred. Both of these factors depend on the virus and the type of infected cells.

Of note, the spread of two human retroviruses that infect leukocytes, HIV-1 and HTLV-1, occurs between mobile cells forming dynamic contacts with other cells. Both retroviruses cause severe chronic viral infections. Their transmission between individuals occurs through sexual contact and blood transfusion, and vertically from mother to child, including through breastfeeding. In addition to HTLV-1 dissemination through division of infected cells carrying viral genomes, transmission of HTLV-1 viral particles is known to occur mainly through cell contact in vitro and in vivo, with the exception of dendritic cells, which can be infected by cell-free viral particles. By contrast, HIV-1 spread can occur by both diffusion and direct cell–cell transfer. Nevertheless, compelling evidence indicates that direct spread through cell contact is the most efficient mode of HIV-1 dissemination in vitro, and might play a crucial role in vivo:

Can viruses form biofilms? Trends Microbiol. Mar 31 2011
The recent finding that the human T-cell leukemia virus type 1 (HTLV-1) encases itself in a carbohydrate-rich adhesive extracellular ‘cocoon’, which enables its efficient and protected transfer between cells, unveiled a new infectious entity and a novel mechanism of viral transmission. These HTLV-1 structures are observed at the surface of T cells from HTLV-1-infected patients and are reminiscent of bacterial biofilms. The virus controls the synthesis of the matrix, which surrounds the virions and attaches them to the T cell surface. We propose that, similar to bacterial biofilms, viral biofilms could represent ‘viral communities’ with enhanced infectious capacity and improved spread compared with ‘free’ viral particles, and might constitute a key reservoir for chronic infections.

Combination antiretroviral therapy for HIV-1 infection has resulted in profound reductions in viremia and is associated with marked improvements in morbidity and mortality. Therapy is not curative, however, and prolonged therapy is complicated by drug toxicity and the emergence of drug resistance. Management of clinical drug resistance requires in depth evaluation, and includes extensive history, physical examination and laboratory studies. Appropriate use of resistance testing provides valuable information useful in constructing regimens for treatment-experienced individuals with viremia during therapy. This review outlines the emergence of drug resistance in vivo, and describes clinical evaluation and therapeutic options of the individual with rebound viremia during therapy.

Clinical Management of HIV Drug Resistance. Viruses 2011, 3(4), 347-378; doi:10.3390/v3040347

“New diagnoses for people infected with HIV in the UK almost doubled over the past decade, (from 1,950 in 2001 to 3,780 in 2010) according to new figures released today by the Health Protection Agency (HPA). If these 3,780 UK-acquired HIV cases in 2010 had been prevented, over £32 million annually or £1.2 billion over a lifetime in costs would have been saved. Men who have sex with men remain the group most at risk of becoming infected with HIV in the UK and new diagnoses in this group alone have increased by 70 per cent in the past 10 years rising from 1,810 in 2001 to 3,080 in 2010. Late diagnosis continues to severely affect the health outcomes of people with HIV. On average, of all those who die from HIV infection every year, three out of five are diagnosed late – that is after the point their treatment should have begun. New guidance released today by the National Institute of Clinical Excellence recommends increased testing of HIV in key risk groups. In the UK black Africans and men who have sex with men are most at risk of becoming infected with HIV. Increased testing will encourage early diagnosis in these groups.”

via HPA – UK-acquired HIV nearly doubles in ten years

“Rather than destroying HIV, a proposed treatment would embrace its infectious abilities, sending the virus into competition with a harmless, stripped-down version of itself. Dubbed therapeutic interfering particles, or TIPs, these engineered viral scraps would ride with HIV as it spreads from person to person. By out-competing HIV for cellular resources, the TIPs might slow its progression and lower infection rates. “A virus can’t replicate without a host, and similarly TIPs can’t replicate without HIV. It would piggyback on the virus,” said biophysicist and virologist Leor Weinberger of the University of California, San Diego, who modeled the epidemiology of TIPs in a study March 17 in PLoS Computational Biology. “It’s basically a virus of a virus.” Approximately 33 million people now carry HIV, or human immunodeficiency virus, which infects immune system cells that defend against disease. The virus gradually destroys them, taking away the body’s ability to protect itself. Without treatment, HIV infection leads to AIDS in about 10 years. Death follows soon after as common diseases overcome the body.”

via Piggyback Virus Could Curb HIV Pandemic | Wired.com

Source:
Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies. (2011) PLoS Comput Biol 7(3): e1002015. doi:10.1371/journal.pcbi.1002015