TAG HIV Basic Science, Vaccines, and Cure Project Blog

New Paper Rekindles Debate on HIV Replication During ART

For many years scientists have probed the question of whether combination antiretroviral therapy (ART) completely inhibits all HIV replication in the body. The preponderance of evidence has suggested that it does, and opinion has generally tilted toward the idea that persistent virus replication in the face of ART is relatively uncommon. The evidence includes studies of ART intensification (adding multiple drugs to standard combinations), which in most—but not all—cases have documented no effect on levels of residual HIV, as well as genetic studies showing a lack of viral evolution over time in people on long-term treatment. The question remains controversial, however, and some scientists continue to believe that low-level ongoing HIV replication on ART may occur in hard-to-access sites in the body.

A paper published online last week by Nature (and published in this week’s issue) has generated substantial debate and media coverage by claiming to provide evidence that HIV replication persists in lymphoid tissue sites where ART penetration may be limited. The study involves a very small sample size of just three people, who had only been taking ART for six months. Complex genetic analyses of HIV sequences sampled from these individuals indicated continuing evolution of several viral lineages, and also provided evidence of trafficking of these viruses from the lymphoid tissue to the blood.

To help explain the findings, the researchers developed a model showing that suboptimal penetration of ART into tissues may allow ongoing low-level HIV replication without necessarily leading to the emergence of drug-resistant viruses (one of the arguments against ongoing replication is based on the expectation that drug resistance would eventually be seen).

The paper’s authors appear confident that these findings are generalizable to most people on ART, but other scientists are skeptical – some vociferously so. In an article about the study by Jon Cohen in Science, longtime HIV researcher John Mellors states that the results contrast with those of his own group, and argues strongly that “the authors should be much more cautious.” Given the small number of individuals included in the Nature paper and the relative short duration of ART, this point seems very reasonable. Larger studies will be needed to resolve the controversy, and will likely be forthcoming soon.

Pending additional data, the implications for cure research are unclear. If persistent HIV replication on ART is sustaining the reservoir of infected cells, as the new paper suggests, then novel strategies may be needed to suppress the virus in tissues. On the other hand, the goal of the “kill” element in the “kick & kill” approach to HIV reservoir reduction (currently being pursued by many scientists) is to eliminate HIV-infected cells that are expressing viral antigens. And theoretically, at least, successful “kill” approaches should also be able to target cells where persistent HIV replication is occurring because they would be expected to display viral antigens.

Nature (2016) doi:10.1038/nature16933

Received 06 July 2015 Accepted 18 December 2015 Published online 27 January 2016

Persistent HIV-1 replication maintains the tissue reservoir during therapy

Ramon Lorenzo-Redondo, Helen R. Fryer,  Trevor Bedford, Eun-Young Kim, John Archer, Sergei L. Kosakovsky Pond, Yoon-Seok Chung, Sudhir Penugonda, Jeffrey G. Chipman, Courtney V. Fletcher, Timothy W. Schacker, Michael H. Malim, Andrew Rambaut, Ashley T. Haase, Angela R. McLean & Steven M. Wolinsky

Abstract

Lymphoid tissue is a key reservoir established by HIV-1 during acute infection. It is a site associated with viral production, storage of viral particles in immune complexes, and viral persistence. Although combinations of antiretroviral drugs usually suppress viral replication and reduce viral RNA to undetectable levels in blood, it is unclear whether treatment fully suppresses viral replication in lymphoid tissue reservoirs. Here we show that virus evolution and trafficking between tissue compartments continues in patients with undetectable levels of virus in their bloodstream. We present a spatial and dynamic model of persistent viral replication and spread that indicates why the development of drug resistance is not a foregone conclusion under conditions in which drug concentrations are insufficient to completely block virus replication. These data provide new insights into the evolutionary and infection dynamics of the virus population within the host, revealing that HIV-1 can continue to replicate and replenish the viral reservoir despite potent antiretroviral therapy.

HIV Cure Research Reviews in the Journal of Clinical Investigation

The Journal of Clinical Investigation has published a collection of reviews on HIV cure research edited by Robert Siliciano. The articles are not open access unfortunately, but a day pass for the journal’s website (which allows downloading of all PDFs) costs $10 which is relatively affordable compared to many other publishers. 

Recent developments in the effort to cure HIV infection: going beyond N = 1

Janet D. Siliciano, Robert F. Siliciano

J Clin Invest. 2016;126(2):409-414. doi:10.1172/JCI86047.

Towards HIV-1 remission: potential roles for broadly neutralizing antibodies

J Clin Invest. 2016;126(2):415-423. doi:10.1172/JCI80561.

In vivo platforms for analysis of HIV persistence and eradication

Victor Garcia

J Clin Invest. 2016;126(2):424-431. doi:10.1172/JCI80562.

Hematopoietic stem cell transplantation for HIV cure

Daniel R. Kuritzkes

J Clin Invest. 2016;126(2):432-437. doi:10.1172/JCI80563.

The role of HIV integration in viral persistence: no more whistling past the proviral graveyard

Frank Maldarelli

J Clin Invest. 2016;126(2):438-447. doi:10.1172/JCI80564.

Molecular mechanisms of HIV latency

Daniele C. Cary, Koh Fujinaga, B. Matija Peterlin

J Clin Invest. 2016;126(2):448-454. doi:10.1172/JCI80565.

HIV-specific CD8+ T cells and HIV eradication

Brad Jones, Bruce D. Walker

J Clin Invest. 2016;126(2):455-463. doi:10.1172/JCI80566.

Measuring the latent reservoir in vivo

Marta Massanella, Douglas D. Richman

J Clin Invest. 2016;126(2):464-472. doi:10.1172/JCI80567.

A Trio of Papers Provide New Insights Into Host Cell Manipulation by HIV

Viruses are notorious for manipulating host cells in ways that favor viral replication, and HIV is no exception. The HIV protein Nef has a well-described capacity to subvert normal cellular biology, including down-regulating cell surface class I HLA molecules that might otherwise allow CD8 T cells to recognize that the cell is infected. Last week saw the publication of three independent studies that all report the discovery of another important Nef function.

Two papers in Nature describe the use different techniques to converge on the finding that Nef diverts cellular proteins named serine incorporator (SERINC) 5 and SERINC3 away from the cell membrane, thus preventing their incorporation into budding HIV virions. In the absence of this diversionary Nef activity, the proteins—particularly SERINC5—dramatically impair HIV infectivity. The mechanism by which incorporation of the SERINC proteins compromises HIV is now under investigation. The phenomenon appears relevant to a broad range of enveloped retroviruses, because occlusion of SERINC5 was found to be a conserved function of Nef proteins encoded by multiple primate immunodeficiency viruses and was also accomplished by the structurally distinct Gag protein of murine leukemia virus.

The third paper, an open access publication in Cell Host & Microbe, also identified SERINC3/5 as targets of Nef using a proteomic analysis of alterations to the T cell surface caused by HIV infection. Additionally, the researchers discovered that HIV’s Vpu protein significantly downregulates SNAT1 (Sodium Coupled Neutral Amino Acid Transporter 1), a protein involved in amino acid metabolism, thereby impairing T cell proliferation. Interestingly, this capacity of Vpu appears to have been acquired relatively recently in evolutionary time as it is restricted to viral variants from the SIVcpz/HIV-1 lineage. Given that this lineage is responsible for the HIV pandemic, the researchers note that Vpu’s acquisition of the ability to downregulate SNAT1 may have contributed to the spread of the virus in the human population.

The apparent importance of these host cell manipulations in the HIV life cycle suggests that targeted inhibition of Nef and/or Vpu might have therapeutic potential, and further studies are planned.

Cell Host & Microbe 18, 1–15

Open Access

DOI: http://dx.doi.org/10.1016/j.chom.2015.09.003

Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef

Nicholas J. Mathesonl, Jonathan Sumner, Kim Wals, Radu Rapiteanu, Michael P. Weekes, Raphael Vigan, Julia Weinelt, Michael Schindler, Robin Antrobus, Ana S.H. Costa, Christian Frezza, Clary B. Clish, Stuart J.D. Neil, Paul J. Lehner 

Summary 

Critical cell surface immunoreceptors downregulated during HIV infection have previously been identified using non-systematic, candidate approaches. To gain a comprehensive, unbiased overview of how HIV infection remodels the T cell surface, we took a distinct, systems-level, quantitative proteomic approach. >100 plasma membrane proteins, many without characterized immune functions, were downregulated during HIV infection. Host factors targeted by the viral accessory proteins Vpu or Nef included the amino acid transporter SNAT1 and the serine carriers SERINC3/5. We focused on SNAT1, a β-TrCP-dependent Vpu substrate. SNAT1 antagonism was acquired by Vpu variants from the lineage of SIVcpz/HIV-1 viruses responsible for pandemic AIDS. We found marked SNAT1 induction in activated primary human CD4+ T cells, and used Consumption and Release (CoRe) metabolomics to identify alanine as an endogenous SNAT1 substrate required for T cell mitogenesis. Downregulation of SNAT1 therefore defines a unique paradigm of HIV interference with immunometabolism.

Nature. 2015 Sep 30. doi: 10.1038/nature15400. [Epub ahead of print]

SERINC3 and SERINC5 restrict HIV-1 infectivity and are counteracted by Nef.

Usami Y, Wu Y, Göttlinger HG.

Abstract

HIV-1 Nef and the unrelated mouse leukaemia virus glycosylated Gag (glycoGag) strongly enhance the infectivity of HIV-1 virions produced in certain cell types in a clathrin-dependent manner. Here we show that Nef and glycoGag prevent the incorporation of the multipass transmembrane proteins serine incorporator 3 (SERINC3) and SERINC5 into HIV-1 virions to an extent that correlates with infectivity enhancement. Silencing of both SERINC3 and SERINC5 precisely phenocopied the effects of Nef and glycoGag on HIV-1 infectivity. The infectivity of nef-deficient virions increased more than 100-fold when produced in double-knockout human CD4+ T cells that lack both SERINC3 and SERINC5, and re-expression experiments confirmed that the absence of SERINC3 and SERINC5 accounted for the infectivity enhancement. Furthermore, SERINC3 and SERINC5 together restricted HIV-1 replication, and this restriction was evaded by Nef. SERINC3 and SERINC5 are highly expressed in primary human HIV-1 target cells, and inhibiting their downregulation by Nef is a potential strategy to combat HIV/AIDS.

Nature. 2015 Sep 30. doi: 10.1038/nature15399. [Epub ahead of print]

HIV-1 Nef promotes infection by excluding SERINC5 from virion incorporation.

Rosa A, Chande A, Ziglio S, De Sanctis V, Bertorelli R, Goh SL, McCauley SM, Nowosielska A, Antonarakis SE, Luban J, Santoni FA, Pizzato M.

Abstract

HIV-1 Nef, a protein important for the development of AIDS, has well-characterized effects on host membrane trafficking and receptor downregulation. By an unidentified mechanism, Nef increases the intrinsic infectivity of HIV-1 virions in a host-cell-dependent manner. Here we identify the host transmembrane protein SERINC5, and to a lesser extent SERINC3, as a potent inhibitor of HIV-1 particle infectivity that is counteracted by Nef. SERINC5 localizes to the plasma membrane, where it is efficiently incorporated into budding HIV-1 virions and impairs subsequent virion penetration of susceptible target cells. Nef redirects SERINC5 to a Rab7-positive endosomal compartment and thereby excludes it from HIV-1 particles. The ability to counteract SERINC5 was conserved in Nef encoded by diverse primate immunodeficiency viruses, as well as in the structurally unrelated glycosylated Gag from murine leukaemia virus. These examples of functional conservation and convergent evolution emphasize the fundamental importance of SERINC5 as a potent anti-retroviral factor.