8.4 Robert Siliciano — The Challenge of the HIV Reservoir

Bob Siliciano: [00:00:00] How about now? Now good? I realized that our work has been very heavily dependent on the contributions of many people in this room. I'd like to argue that the main barrier to curing HIV infection is a small pool of resting memory T cells that harbor a latent form of the viral genome. Resting lymphocytes are among the most quiescent cells in the body. It is the unique physiology of these cells that allows HIV to establish a state of [00:00:30] latent infection somewhat unexpectedly.

Now, the idea of latency and lentiviral infections goes back to some studies by Ashley Haase, of visna virus infection in sheep, showing that the number of cells with viral DNA was considerably greater than the number of cells expressing viral RNA. (1) In early studies, Bob [Gallo] and Flossie [Wong-Staal] showed that the same thing was true in HIV infection. (2) And a number of [00:01:00] studies from the [Tony] Fauci group then showed that HIV gene expression could be upregulated in infected T cell lines by various cytokines. (3)

But in the early 1990s, studies from Jeff Lifson and John Mellors showed that HIV replication is active throughout the course of the infection and drives a CD4 depletion. So HIV persistence doesn't depend on latency. [00:01:30] The virus replicates continuously and persists by evading the immune response through rapid evolution, as shown by George [Shaw], Dennis [Burton], Bruce [Walker], and many others.

I think we didn't fully appreciate this paradox when we began to consider models of how latent infection could be established, models that looked something like this. (4) They viewed latency in the context of the normal physiology of [00:02:00] CD4 cells, where naive CD4 cells respond to antigen, become activated and generate effector cells, most of which die, but some survive and revert to a quiescent state as long-lived memory cells, allowing future responses to the same antigen. The virus replicates preferentially in the activated cells, and as we've heard, they die very quickly, as shown by David [Ho] and George. Mario Stevenson had shown that direct infection resting cells is blocked at a stage prior to [00:02:30] integration. And we know, from recent work from Warner Green, that many of these cells die by pyroptosis. But if they are activated before that, they can complete the virus life cycle. This represents a phase of pre-integration latency.

We hypothesized that a more stable form of latency might arise if some infected cells with integrated provirus survived long enough to return to a quiescent state. In this state, transcription factors like NF-κB [00:03:00]needed for HIV gene expression, as shown by Warner and others, are excluded from the nucleus, and levels of P-TEFb are very low as shown by Andrew Rice . Therefore, the return to quiescence is actually, essentially, automatically, enforces this state of latency. And then if these cells are activated by antigen, again, they can go on to produce a virus.

This is post-integration latency. The nice thing about this model is it allows us to [00:03:30] understand HIV persistence really in the context of the normal mechanisms of homeostasis that maintain immunologic memory.

To prove this model, we needed to do three things: we had to isolate very pure populations of resting cells and show they didn't produce any virus, show that the viral genome was integrated into the host cell DNA in these cells, and that you could rescue infectious virus by activating the cells.

The cells are purified using a combination of [00:04:00] magnetic bead depletion and cell sorting. These purified resting cells don't produce virus. We could show they contain integrated provirus by an inverse PCR method that amplifies the junction between host DNA and the provirus. And most importantly, we showed that although these cells don't produce a virus, if you activate them through the T cell receptor, then you can recover an infectious virus.

Diana Finzi, a graduate student in the lab, converted this type of experiment into [00:04:30] a quantitative assay for lately infected cells, known as the Quantitative Viral Outgrowth Assay or Q-VOA, which is still considered the definitive assay for this reservoir. In this assay, you take resting cells, plate them in limiting dilution, and then activate them under conditions where 100% of the cells undergo blast transformation, become activated, and cells with latent provirus will begin to produce virus, which you can amplify by adding CD4 cells to the culture and essentially, grow out, from a single [00:05:00] lately infected cell, enough virus to detect by p24 ELISA two weeks later. (5, 6)

Using this assay, we showed that these cells are present in everybody with HIV infection, you can calculate the frequency. The number that we kept getting was one in a million. This is the number which has made our lives miserable in the subsequent 20 years. These cells are rare and hard to study. This is a very small population of cells, probably not important at all in the natural history of the infection. [00:05:30] It's only important if you want to try to cure the infection.

Our first paper describing the quantitation of these lightly infected cells (5) appeared in the same issue of Nature as this landmark paper from Alan [Perelson] and David [Ho], showing the biphasic decay of viremia in people on the new combination therapy regimens. (7) And so the question immediately became, "Would this latent reservoir persist in people on [00:06:00] antiretroviral therapy?"

With the help of David and many others, we looked for patients who had gone on treatment and had done very well with no evidence of residual virus. You can imagine the tension in the lab when Diana Finzi did the viral outgrowth assay on the first of these patients. This was somebody who had done so well, was essentially thought to have been cured. The last step in this assay is in ELISA, in which you look for [00:06:30] a color change indicating the presence of the virus. Relative to the standards, and Diana saw something like this, she burst into my office with this disturbing news. And I think a similar scene was probably going on in laboratories of Tony Fauci and Doug Richman, who had adopted the viral outgrowth assay and were doing the same kinds of experiments. Later that year, three papers were published, demonstrating persistence of HIV in patients on a suppressive [00:07:00] antiretroviral therapy. (6, 8, 9)

This was the beginning of the Dark Ages for HIV cure research because, as you can see from these old slides, as we accumulated more data, first, in cross-sectional studies and then longitudinal studies, it became clear that this latent reservoir wasn't going away, with a half-life much longer than those of the first and second phase decay defined in Alan's study, longer even then the intermitotic half-life [00:07:30] of memory T cells. (6, 10, 11) We estimated a half-life of 44 months, long enough to ensure lifetime persistence of this reservoir in the setting of optimal treatment. Now, these results were published in 1999 and 2003. Interestingly, David Margolis has recently repeated these studies in a study published last year. (12) Many of the patients in his study were on newer regimens. You can see [00:08:00] that he got exactly the same half-life.

What this says is that all of the remarkable improvements in antiretroviral therapy as a result of the work from John [Martin] and Daria [Hazuda] and many others have really dramatically changed treatment to the point where life expectancies are approaching normal, drug resistance is going away, actually. But those improvements haven't impacted this problem, which is the persistence of a non-replicating form [00:08:30] of the virus.

Now, another thing that became clear very early on from the work of John Mellors, John Coffin, and others was that what antiretroviral therapy really does is to drop the level of plasma virus down to a new steady-state that's just below the limit of detection of the clinical assay. It's about one copy per mil. This, initially, raised concern that the virus is continuing to replicate at a low level. In a series of papers [00:09:00] that, as far as I can tell, have never been read by anyone, we attempted to sequence this trace level of a free virus and learn about its characteristics. (13, 14, 15, 16, 17, 18) What we found was that it was drug-sensitive virus, it was non-evolving, and archival in character, consistent with the idea that it simply represents the activation of a small number of lately infected cells every day. Those cells produce virus which can't infect new cells but which can be detected with a [00:09:30] sensitive-enough assay.

Now, this didn't completely resolve the issue of whether the virus was continuing to replicate. In one additional experiment that a lot of people thought would help to solve this issue was an intensification of treatment by adding a fourth drug from a different class to see whether the residual viremia went down at all. In collaboration with John Coffin and John Mellors, we did this and showed that actually, it doesn't go down at all. (19) This was confirmed in many subsequent studies. Intensification doesn't reduce [00:10:00] this. In fact, no amount of additional antiretroviral drugs will ever reduce residual viremia below this level because this virus is coming from cells that were infected before a treatment was started.

What does this look like? Here's a phylogenetic tree from a single patient. In black are sequences from resting CD4 cells and other cells in the blood, and in the colored triangles are sequences of this free plasma virus. (17, 18) You can see in some cases the sequences are identical, consistent with the idea that the residual viremia is derived from activation of [00:10:30] latently infected cells.

But this is only part of the story. I'm showing you only half of the tree, the rest of the tree is here. What we saw in this patient and in about half the patients we studied was that the plasma virus was dominated by a small number of clones, where we would get the identical viral sequence in many independent limiting dilution analysis over a period of months to years, and these sequences did not show [00:11:00] evidence of evolution. We thought at the time that they might represent the clonal expansion of individual infected cells, and I'll come back to that in a second.

Now, these results suggest that antiretroviral therapy does a very good job of stopping viral replication. We wanted to quantitate, how well do the drugs actually inhibit replication? In another series of papers, which as far as I can tell haven't been read, we analyzed the dose-response curves of antiretroviral drugs. (20, 21, 22) This is the dose-response curve [00:11:30] of a hypothetical antiviral drug with infectivity decreasing as drug concentration increases. You can describe this with the median effect equation, which has an exponent M describing the slope or steepness of the curve. Typically, the values are 1, unless there's some kind of cooperativity going on which will make the slope steeper. This is analogous to the Hill coefficient. It doesn't look like it makes much difference because the curves all come [00:12:00] together in this at higher concentrations, for example, the clinical concentration, this pink-shaded range.

But it actually doesn't make any sense to plot inhibition of viral replication on a linear 1 to 100 scale as pharmacologists always do because viral replication is exponential. So if you simply log-transform these curves, the y-axis, the result is actually pretty shocking. What happens is that the curves diverge dramatically in a clinically relevant concentration range so that drugs with a [00:12:30] higher value of the slope parameter cause much more inhibition, actually by orders and orders of magnitude. By this analysis, the slope parameter should be a really critical determinant of antiviral activity.

Interestingly, it had never been measured. Lin Shen in our group did this to see whether the values were different from the expected value of one. (20) It turned out that for three classes of antiretroviral drugs, the values were actually much higher. When infectivity was the readout, there was evidence of cooperative dose-response curves. [00:13:00] If you plug these values into the median effect equation, you can see that some classes of antiretroviral drugs produced enormously high levels of inhibition. This y-axis here is logs of inhibition of a single round of infection. You can get up to 10 logs of inhibition by some of the best protease inhibitors at peak plasma concentrations, just truly phenomenal levels of inhibition. The integrase inhibitors actually have lower slope values but work well due to synergistic effects. [00:13:30] 

The bottom line of this is that antiviral drugs have a much greater ability to block viral replication than I think was previously appreciated. And this analysis is now being applied to broadly neutralizing antibodies and also to hepatitis C drugs. (23) This is a virus that causes high viremia, rapid evolution, and resistance with sub-optimal treatment. But, as you know, we're getting cure rates approaching 100% with two-drug regimens. I think HIV would be similarly curable if [00:14:00] it weren't for the latent reservoir, which—hepatitis C doesn't have a latent form like this. So antiretroviral therapy effectively stops viral replication, except in a couple of situations. Of course, when there's poor adherence, there may be tissue sites where there's poor penetration of antiretroviral drugs. (24) And cell-to-cell spread, as shown by Dr. [David] Baltimore, is more difficult to inhibit with antiretroviral drugs. (25) [00:14:30] 

Back to the Dark Ages now. This is 2005 when this paper appeared from the lab of David Margolis, suggesting that the latent reservoir could be decreased by treatment of patients with a histone deacetylase inhibitor, valproic acid. (26) And although our laboratory couldn't confirm these findings , I think this was actually a very important paper because a cure was mentioned in the title. Essentially, [00:15:00] it said that this is something that we should and could try to do. David went on to be a real leader in the HIV cure field along with people like Steve Deeks and Sharon Lewin, who will speak next, Françoise [Barré-Sinoussi] and the International AIDS Society, the NIH funding, the Martin Delaney Collaboratories, and amfAR, which has given us a very ambitious goal for cure research.

Now, the other thing that really [00:15:30] I think turned things around was, of course, the cure of Timothy Brown (1966–2020) with a stem cell transplant. (27) Now interestingly, I think some of the most informative cases related to this are the near-cure cases. For example, the two Boston patients reported by Tim Henrich. (28) These patients received an allogeneic stem cell transplant from donors who are wild-type for CCR5, and antiretroviral therapy was continued throughout the transplant period to prevent [00:16:00] infection of donor cells. Then, after a couple of years treatment was stopped. The rebound that normally happens at two weeks didn't occur, and instead, these patients went for, in one case, eight months before a sudden and dramatic rebound in viremia. We think that this is due to the persistence of a small number of latently infected host cells, one of which became activated.

Similarly, the Mississippi baby [00:16:30] reported by my Hopkins colleague, Debbie Persaud. (29) This an infant treated on day one, viral load went down to undetectable levels, and then remained there until, at 18 months, treatment was stopped against medical advice, but there was no rebound for a period of over two years when there was a sudden, again, and dramatic rebound and viremia.

What's interesting in these three cases is that there was essentially no immune response to the virus, no adaptive immune response due to the early [00:17:00] treatment, or the transplantation process. In the absence of an immune response and in the absence of antiviral therapy, viral replication should be exponential. Really, the only way to explain persistence in these cases is that there was a latent form that could persist and then for up to years and then begin to replicate.

What are we going to do about this? Sharon [Lewin] will describe some of the approaches including the shock and kill approach to purge cells out of [00:17:30] the latent reservoir. In our own studies, we've shown that many latency-reversing agents actually work very poorly, relative to T-cell activation, when tested ex-vivo using patient cells. (29) But you can find some combinations, particularly those that include a protein kinase C agonists. (30) This makes a lot of sense because those drugs activate some of the downstream signaling pathways downstream of the T cell receptor. Reversing latency is not all that we have to [00:18:00] do, because we've shown CTL T cells for most patients on treatment are actually fairly ineffective at killing cells once latency is reversed. (31) Part of the problem is that the latent reservoir is actually dominated by sequences that have escape mutations in major CTL epitopes. (32)

In the remaining time, I want to talk about the issue of, how do we measure the reservoir? There's no doubt, as has been mentioned, that the viral load assay developed by Jeff Lifson greatly [00:18:30] sped the development of antiviral drugs because you could tell right away whether the drugs were working. We need such an assay for the latent reservoir. This viral outgrowth assay, although it always works, nobody wants to do it. It's labor-intensive and poorly scalable. Many people use PCR, but we've shown in a comparative study that DNA PCR assays for provirus [00:19:00] give infective cell frequencies that are about 300-fold higher than and poorly correlated with the viral outgrowth assay. (33)

What does this mean? It means that there's a large number of proviruses that don't score in the viral outgrowth assay, these are non-induced proviruses. (34) And by full-length single genome sequencing, we've shown that the vast majority of these proviruses are defective either due to [00:19:30] APOBEC-3G-mediated hypermutation, as shown in green, or due to large internal deletions [00:19:36] caused by a copy choice recombination during reverse transcription. (35) Those are shown in white. It's actually hard to find an intact provirus.

If you measure the total number of infected cells by a digital droplet PCR assay such as those developed by Doug Richman, it looks like this. (34, 35) The quantitative viral outgrowth assay on the same patients gives [00:20:00] this frequency. And then if you measure the number of intact proviruses by this full-length single genome sequencing, you get something in the middle. This difference is actually due to these over defects that I mentioned. This difference is due to the fact that there's a large number of proviruses that appear to be intact but are not induced by a single round of T cell activation.

And so we asked whether these viruses were replication-competent, and could be induced? [00:20:30] By simply reconstructing them through gene synthesis, we've shown that the vast majority of the intact ones can replicate if reconstructed and introduced through transfection. Then to see whether they can be induced, we've done repetitive stimulation assays where you take the cells in the negative wells from the viral outgrowth assay and simply stimulate them again and see whether you can bring out additional proviruses.

The result is that [00:21:00] you can, as shown in hatched bars. Each simulation brings out additional proviruses. What it really looks like is this. The latent reservoir is larger than was estimated through the viral outgrowth assay. It's something like this. The upper limit is set by the number of intact proviruses, in blue. But with current assays, we can bracket but not precisely determine the size of the reservoir. There may be some intact proviruses that are just permanently silenced through epigenetic [00:21:30] mechanisms.

Now, one of the other things that fell out of this was that this gave us a unique opportunity to have a very large number of independent isolates of replication-competent virus from the same patient, which is something that's difficult to do because of the low frequency of these cells. One thing that became immediately apparent was that many of these isolates had identical envelope sequence. And then through collaboration with Brandon Keele, [00:22:00] we showed that when the sequence was identical in the envelope region in general, it was identical throughout the entire provirus. (36)

There's really two explanations for having a large number of independent isolates with identical sequence from somebody who has had extensive diversification over time, such as this patient. One idea is that there's a dominant virus population that infects a large number of cells that then become latent. [00:22:30] The other idea is that a single infected cell proliferates after infection, copying the viral genome into many progeny cells.

Now, we can distinguish this through phylogenetics, because if the former hypothesis is correct, then one-third of the newly infected cells, based on the error rate of rT should have a point mutation, and there should be, in other words, a large number of sequences that are close to the dominant sequence. In fact, that's not what you see. [00:23:00] The dominant sequence, if you compare intra-patient genetic distances between isolates, there's actually very few sequences that are close to the dominant sequences.

We think that this represents clonal expansion. If you add up the number of independent isolates that belong to these expanded clones, it's actually over half. In other words, most of the latent reservoir actually results from proliferation of a smaller number of previously [00:23:30] infected cells, rather than direct infection. This result is consistent with the results from our analysis of residual viremia that I mentioned and with the elegant integration site analysis done by Frank Maldarelli and by Lisa Frenkel's group. (37, 38)

I think our work extends this work by showing that these expanded clones actually include clones with a replication-competent virus, and I think John's lab has recently come to a very [00:24:00] similar conclusion. There are some people who think that this is very bad news, almost the beginning of another Dark Ages. I think we have to remember that the total size of the reservoir in our hands never really increases. It's maintaining a roughly constant level. So that this proliferation has to be balanced by a loss of cells. We really need to understand what's causing that loss. How can we take advantage of that?

I'm going to stop [00:24:30] there. I thank the people involved in this work. I've been working on this problem with my wife, Janet, for many years. I mentioned some of the people already. The pharmacodynamic work was done by Ben Jerik and Lin Shen, Ya Chi Ho has done the work on defective proviruses along with Katie Bruner. I want to thank many collaborators, including Steve Deeks, Brandon, who's here, Doug Richman, John, and many others. I'll stop there, I'd be happy to try and answer any questions.

[applause] 

[00:25:00] Alan Perelson (Moderator): We have time for some questions. There's a question over in the—Wait, wait for the microphone, please.

Audience 1: Thank you. I was wondering, what is your take on how these latent reservoirs are established? Is it possible for an already replicating [00:25:30] provirus to go into latency. any epigenetic marks and things like that?

Bob Siliciano: Yes. We think the establishment, actually, is an unfortunate accident of the timing of events after activation. CCR5 levels come up fairly slowly. Then, as the cell is reverting back to a quiescent state, reverse transcription efficiency decreases due to decrease in [00:26:00] nucleotide concentrations, and NFκB gene expression falls fairly quickly. So that if cells are infected in a narrow window, which in our hands is between six and nine days after infection, then the yield of latently infected cells is actually the highest. It's really an unfortunate accident of timing. There's a lot of debate about whether latency is something that evolved. We actually don't think so. We think that this is a—This phenomenon I've been studying for my whole [00:26:30] career is really an epi-phenomenon that's not particularly important, except that it's what's left when you stop viral replication.

Alan: Ruth?

Ruth Ruprecht: Hi, beautiful work. We looked at the distribution of full-length proviral DNA in the SIVmac239 rhesus monkey model, during the proof of concept experiment to tell [Peter] Duesberg (b. 1936) that it's the virus, stupid, it's [00:27:00] the provirus, rather stupid. We actually had these animals that were inoculated with pure, super coiled SIVmac239 plasmid DNA. We then followed the animals prospectively in lymph nodes and in peripheral blood for the presence of full-length proviruses, by long-distance PCR and small PCR.

It turned out that, first of all, within four weeks, 90% of the proviruses [00:27:30] were now deleted, shorter. Number two, during what was called the chronic stage of infection, the full-length proviruses predominated in lymph nodes, and they were much less prevalent—The ratio of full-length to deleted proviruses was very different in the peripheral blood. But then during the end-stage, and when the animals had AIDS, the ratio equalized again. There is an implication that there is [00:28:00] a selective pressure on full-length provirus containing cells in the blood, but not in the lymph nodes.

Bob: We've actually seen something very similar with SIV. Clearly, the same types of defects arise and dominate in resting CD4 cells.

Bob Gallo: Bob, this is a speculative thing. There's such a small number, I would think it wouldn't matter, but I would like to get your feeling for it and that's, do you think there's any clinical impact [00:28:30] of the defective proviruses, just running around in someone? Let's say there was, you conquered everything, there's a functional cure, there's no more virus, but there's X number of defective proviruses integrated in somebody's cells. I don't mean getting more cancer. Just in general, do you have a feeling for it? I suppose it could be studied by balancing the amount of virus in anybody and controlling it, determining what your estimate is to the defectives, and looking at [00:29:00] clinical course, but it'd be a lot of work, of course.

Bob Siliciano: There's some suggestion from Cliff Lane's group that these can be expressed, that the LTRs are generally functional. When we've looked at the level of expression of HIV RNA from defective proviruses, it's generally very, very low.

Bob Gallo: What kind of expression? Just that they're there.

Bob Siliciano: Just their presence.

Bob Gallo: Just [unintelligible 00:29:23] of DNA that might have set some genome regulations or some form [crosstalk] [00:29:30]

Bob Siliciano: We haven't. We don't have evidence right now.

Alan: Okay. John?

John Mellors: Bob, that's great. A couple of comments and a question. Remarkably, you threw up 57% of your isolates showed evidence of clonal expansion, and we found 55%, I think. Second, the work with Steve Hughes that's ongoing suggests that [00:30:00] clones don't know whether they're replication-competent or not are established very early after infection. Within weeks, it's possible. And last, this offers opportunity, but also some concern that each infected-cell clone could have unique immunobiology based on integration site and also the type of cell that it's in. [00:30:30] That's the concern that one strategy may successfully eliminate that clone, another may expand it, but I think this allows a closer examination at the clonal level of what our interventions are doing.

Bob: Yes, no, I agree. I think the first thing we have to do is to sort out whether this proliferation is normal homeostatic proliferation versus driven by integration site.

David Baltimore: That's what I was [00:31:00] trying to think about also. It seems to me there are two hypotheses. One is that it's driven by antigen exposure in a memory population, and the other is that it's some sort of clonal proliferation that could be a precursor to an oncogenic process or something. The only way I can think about telling the difference, and I think you may have just answered the question, is whether it's something that develops over time and continually develops new clones or a quasi-clonal process as the patient gets older, or it starts off from the beginning.

Bob: Yes, no, I agree. In our studies of the predominant plasma clones, which I think were an indication of these clonal populations, [00:32:00] what we've seen is actually that they don't continually increase, they can wax and wane. My sense is that this is part of a normal homeostatic process, perhaps driven by an antigen or maybe more likely by the cytokines like IL-7 and IL-15, which can drive these cells to proliferate without actually turning on HIV gene expression, so that their proliferation—

Audience 5: That shouldn't give you a clonal expansion, that should just give you an expansion phase. [00:32:30] It shouldn't favor a clone.

Bob: Yes, I think the entire population is under this homeostatic regulation, and why some clones expand to become dominant is completely unclear.

Alan: Paul's been patient, Paul.

Paul Bieniasz: To try and get at the question, whether there's a contribution of virus replication to residual plasma viremia, if you [00:33:00] look at env sequences—so there's no requirement for an intact env protein to get a plasma RNA molecule, right? If you compare the fraction of sequences that are obviously defective in DNA versus plasma RNA, if you just look at the env gene, you'd expect them to basically be the same. Is that what you see or—

Bob: That's an interesting [00:33:30] point. The problem is, I think, the nature of the defects is either these very large, almost half-genome or near-full genome length deletions or the hypermutation, which puts 20 stop codons in envelope, so that for proviruses to actually produce a plasma virus, they're much more likely to be intact or nearly intact.

Paul: [00:34:00] Do you ever see then defective env sequences in your plasma virus?

Bob: I would say rarely.

Alan: I know there are lots of questions, we have to call it. Thanks so much.

[00:34:18] [END OF AUDIO]

Citations

1. Brahic, Michel, Linda Stowring, Peter Ventura, and Ashley T. Haase. “Gene Expression in Visna Virus Infection in Sheep.” Nature 292, no. 5820 (July 1981): 240–42. doi:10.1038/292240a0.
2. Harper, Mary E., Lisa M. Marselle, Robert C. Gallo, and Flossie Wong-Staal. “Detection of Lymphocytes Expressing Human T-Lymphotropic Virus Type III in Lymph Nodes and Peripheral Blood from Infected Individuals by in Situ Hybridization.” Proceedings of the National Academy of Sciences 83, no. 3 (February 1, 1986): 772–76. doi:10.1073/pnas.83.3.772.
3. Folks, Thomas M., Kathleen A. Clouse, Jesse Justement, Arnold Rabson, Elia Duh, John H. Kehrl, and Anthony S. Fauci. “Tumor Necrosis Factor Alpha Induces Expression of Human Immunodeficiency Virus in a Chronically Infected T-Cell Clone.” Proceedings of the National Academy of Sciences 86, no. 7 (April 1, 1989): 2365–68. doi:10.1073/pnas.86.7.2365.
4. Chun, Tae-Wook, Diana Finzi, Joseph Margolick, Karen Chadwick, David Schwartz, and Robert F. Siliciano. “In Vivo Fate of HIV-1-Infected T Cells: Quantitative Analysis of the Transition to Stable Latency.” Nature Medicine1, no. 12 (December 1995): 1284–90. doi:10.1038/nm1295-1284.
5. Chun, Tae-Wook, Lucy Carruth, Diana Finzi, Xuefei Shen, Joseph A. DiGiuseppe, Harry Taylor, Monika Hermankova, et al. “Quantification of Latent Tissue Reservoirs and Total Body Viral Load in HIV-1 Infection.” Nature 387, no. 6629 (May 8, 1997): 183–88. doi:10.1038/387183a0.
6. Finzi, Diana, Monika Hermankova, Theodore Pierson, Lucy M. Carruth, Christopher Buck, Richard E. Chaisson, Thomas C. Quinn, et al. “Identification of a Reservoir for HIV-1 in Patients on Highly Active Antiretroviral Therapy.” Science 278, no. 5341 (November 14, 1997): 1295–1300. doi:10.1126/science.278.5341.1295.
7. Perelson, Alan S., Paulina Essunger, Yunzhen Cao, Mika Vesanen, Arlene Hurley, Kalle Saksela, Martin Markowitz, and David D. Ho. “Decay Characteristics of HIV-1-Infected Compartments during Combination Therapy.” Nature 387, no. 6629 (May 8, 1997): 188–91. doi:10.1038/387188a0.
8. Chun, Tae-Wook, Lieven Stuyver, Stephanie B. Mizell, Linda A. Ehler, Jo Ann M. Mican, Michael Baseler, Alun L. Lloyd, Martin A. Nowak, and Anthony S. Fauci. “Presence of an Inducible HIV-1 Latent Reservoir during Highly Active Antiretroviral Therapy.” Proceedings of the National Academy of Sciences 94, no. 24 (November 25, 1997): 13193–97. doi:10.1073/pnas.94.24.13193.
9. Wong, Joseph K., Marjan Hezareh, Huldrych F. Günthard, Diane V. Havlir, Caroline C. Ignacio, Celsa A. Spina, and Douglas D. Richman. “Recovery of Replication-Competent HIV Despite Prolonged Suppression of Plasma Viremia.” Science 278, no. 5341 (November 14, 1997): 1291–95. doi:10.1126/science.278.5341.1291.
10. Finzi, Diana, Joel Blankson, Janet D. Siliciano, Joseph B. Margolick, Karen Chadwick, Theodore Pierson, Kendall Smith, et al. “Latent Infection of CD4 + T Cells Provides a Mechanism for Lifelong Persistence of HIV-1, Even in Patients on Effective Combination Therapy.” Nature Medicine 5, no. 5 (May 1999): 512–17. doi:10.1038/8394.
11. Siliciano, Janet D., Joleen Kajdas, Diana Finzi, Thomas C. Quinn, Karen Chadwick, Joseph B. Margolick, Colin Kovacs, Stephen J. Gange, and Robert F. Siliciano. “Long-Term Follow-up Studies Confirm the Stability of the Latent Reservoir for HIV-1 in Resting CD4 + T Cells.” Nature Medicine 9, no. 6 (June 2003): 727–28. doi:10.1038/nm880.
12. Crooks, Amanda M., Rosalie Bateson, Anna B. Cope, Noelle P. Dahl, Morgan K. Griggs, JoAnn D. Kuruc, Cynthia L. Gay, et al. “Precise Quantitation of the Latent HIV-1 Reservoir: Implications for Eradication Strategies.” The Journal of Infectious Diseases 212, no. 9 (November 1, 2015): 1361–65. doi:10.1093/infdis/jiv218.
13. Hermankova, Monika, Stuart C. Ray, Christian Ruff, Monique Powell-Davis, Roxann Ingersoll, Richard T. D’Aquila, Thomas C. Quinn, Janet D. Siliciano, Robert F. Siliciano, and Deborah Persaud. “HIV-1 Drug Resistance Profiles in Children and Adults With Viral Load of <50 Copies/ML Receiving Combination Therapy.” JAMA 286, no. 2 (July 11, 2001): 196–207. doi:10.1001/jama.286.2.196.
14. Persaud, Deborah, Yan Zhou, Janet M. Siliciano, and Robert F. Siliciano. “Latency in Human Immunodeficiency Virus Type 1 Infection: No Easy Answers.” Journal of Virology 77, no. 3 (February 1, 2003): 1659–65. doi:10.1128/JVI.77.3.1659-1665.2003.
15. Kieffer, Tara L., Mariel M. Finucane, Richard E. Nettles, Thomas C. Quinn, Karl W. Broman, Stuart C. Ray, Deborah Persaud, and Robert F. Siliciano. “Genotypic Analysis of HIV-1 Drug Resistance at the Limit of Detection: Virus Production without Evolution in Treated Adults with Undetectable HIV Loads.” The Journal of Infectious Diseases 189, no. 8 (April 15, 2004): 1452–65. doi:10.1086/382488.
16. Nettles, Richard E., Tara L. Kieffer, Patty Kwon, Daphne Monie, Yefei Han, Teresa Parsons, Joseph Cofrancesco, et al. “Intermittent HIV-1 Viremia (Blips) and Drug Resistance in Patients Receiving HAART.” JAMA 293, no. 7 (February 16, 2005): 817–29. doi:10.1001/jama.293.7.817.
17. Bailey, Justin R., Ahmad R. Sedaghat, Tara Kieffer, Timothy Brennan, Patricia K. Lee, Megan Wind-Rotolo, Christine M. Haggerty, et al. “Residual Human Immunodeficiency Virus Type 1 Viremia in Some Patients on Antiretroviral Therapy Is Dominated by a Small Number of Invariant Clones Rarely Found in Circulating CD4+ T Cells.” Journal of Virology 80, no. 13 (July 1, 2006): 6441–57. doi:10.1128/JVI.00591-06.
18. Brennan, Timothy P., John O. Woods, Ahmad R. Sedaghat, Janet D. Siliciano, Robert F. Siliciano, and Claus O. Wilke. “Analysis of Human Immunodeficiency Virus Type 1 Viremia and Provirus in Resting CD4+ T Cells Reveals a Novel Source of Residual Viremia in Patients on Antiretroviral Therapy.” Journal of Virology 83, no. 17 (September 1, 2009): 8470–81. doi:10.1128/JVI.02568-08.
19. Dinoso, J. B., S. Y. Kim, A. M. Wiegand, S. E. Palmer, S. J. Gange, L. Cranmer, A. O’Shea, et al. “Treatment Intensification Does Not Reduce Residual HIV-1 Viremia in Patients on Highly Active Antiretroviral Therapy.” Proceedings of the National Academy of Sciences 106, no. 23 (June 9, 2009): 9403–8. doi:10.1073/pnas.0903107106.
20. Shen, Lin, Susan Peterson, Ahmad R. Sedaghat, Moira A. McMahon, Marc Callender, Haili Zhang, Yan Zhou, et al. “Dose-Response Curve Slope Sets Class-Specific Limits on Inhibitory Potential of Anti-HIV Drugs.” Nature Medicine 14, no. 7 (July 2008): 762–66. doi:10.1038/nm1777.
21. Jilek, Benjamin L., Melissa Zarr, Maame E. Sampah, S. Alireza Rabi, Cynthia K. Bullen, Jun Lai, Lin Shen, and Robert F. Siliciano. “A Quantitative Basis for Antiretroviral Therapy for HIV-1 Infection.” Nature Medicine 18, no. 3 (March 2012): 446–51. doi:10.1038/nm.2649.
22. Rosenbloom, Daniel I. S., Alison L. Hill, S. Alireza Rabi, Robert F. Siliciano, and Martin A. Nowak. “Antiretroviral Dynamics Determines HIV Evolution and Predicts Therapy Outcome.” Nature Medicine 18, no. 9 (September 2012): 1378–85. doi:10.1038/nm.2892.
23. Feld, Jordan J., Ira M. Jacobson, Christophe Hézode, Tarik Asselah, Peter J. Ruane, Norbert Gruener, Armand Abergel, et al. “Sofosbuvir and Velpatasvir for HCV Genotype 1, 2, 4, 5, and 6 Infection.” New England Journal of Medicine 373, no. 27 (December 31, 2015): 2599–2607. doi:10.1056/NEJMoa1512610.
24. Fletcher, Courtney V., Kathryn Staskus, Stephen W. Wietgrefe, Meghan Rothenberger, Cavan Reilly, Jeffrey G. Chipman, Greg J. Beilman, et al. “Persistent HIV-1 Replication Is Associated with Lower Antiretroviral Drug Concentrations in Lymphatic Tissues.” Proceedings of the National Academy of Sciences 111, no. 6 (February 11, 2014): 2307–12. doi:10.1073/pnas.1318249111.
25. Sigal, Alex, Jocelyn T. Kim, Alejandro B. Balazs, Erez Dekel, Avi Mayo, Ron Milo, and David Baltimore. “Cell-to-Cell Spread of HIV Permits Ongoing Replication despite Antiretroviral Therapy.” Nature 477, no. 7362 (September 2011): 95–98. doi:10.1038/nature10347.
26. Lehrman, Ginger, Ian B Hogue, Sarah Palmer, Cheryl Jennings, Celsa A Spina, Ann Wiegand, Alan L Landay, et al. “Depletion of Latent HIV-1 Infection in Vivo: A Proof-of-Concept Study.” The Lancet 366, no. 9485 (August 13, 2005): 549–55. doi:10.1016/S0140-6736(05)67098-5.
27. Hütter, Gero, Daniel Nowak, Maximilian Mossner, Susanne Ganepola, Arne Müßig, Kristina Allers, Thomas Schneider, et al. “Long-Term Control of HIV by CCR5 Delta32/Delta32 Stem-Cell Transplantation.” New England Journal of Medicine 360, no. 7 (February 12, 2009): 692–98. doi:10.1056/NEJMoa0802905.
28. Henrich, Timothy J., Zixin Hu, Jonathan Z. Li, Gaia Sciaranghella, Michael P. Busch, Sheila M. Keating, Sebastien Gallien, et al. “Long-Term Reduction in Peripheral Blood HIV Type 1 Reservoirs Following Reduced-Intensity Conditioning Allogeneic Stem Cell Transplantation.” The Journal of Infectious Diseases 207, no. 11 (June 1, 2013): 1694–1702. doi:10.1093/infdis/jit086.
29. Bullen, C. Korin, Gregory M. Laird, Christine M. Durand, Janet D. Siliciano, and Robert F. Siliciano. “New Ex Vivo Approaches Distinguish Effective and Ineffective Sin gle Agents for Reversing HIV-1 Latency in Vivo.” Nature Medicine 20, no. 4 (April 2014): 425–29. doi:10.1038/nm.3489.
30. Laird, Gregory M., C. Korin Bullen, Daniel I. S. Rosenbloom, Alyssa R. Martin, Alison L. Hill, Christine M. Durand, Janet D. Siliciano, and Robert F. Siliciano. “Ex Vivo Analysis Identifies Effective HIV-1 Latency–Reversing Drug Combinations.” The Journal of Clinical Investigation 125, no. 5 (May 1, 2015): 1901–12. doi:10.1172/JCI80142.
31. Shan, Liang, Kai Deng, Neeta S. Shroff, Christine M. Durand, S. Alireza. Rabi, Hung-Chih Yang, Hao Zhang, Joseph B. Margolick, Joel N. Blankson, and Robert F. Siliciano. “Stimulation of HIV-1-Specific Cytolytic T Lymphocytes Facilitates Elimination of Latent Viral Reservoir after Virus Reactivation.” Immunity 36, no. 3 (March 23, 2012): 491–501. doi:10.1016/j.immuni.2012.01.014.
32. Deng, Kai, Mihaela Pertea, Anthony Rongvaux, Leyao Wang, Christine M. Durand, Gabriel Ghiaur, Jun Lai, et al. “Broad CTL Response Is Required to Clear Latent HIV-1 Due to Dominance of Escape Mutations.” Nature 517, no. 7534 (January 2015): 381–85. doi:10.1038/nature14053.
33. Eriksson, Susanne, Erin H. Graf, Viktor Dahl, Matthew C. Strain, Steven A. Yukl, Elena S. Lysenko, Ronald J. Bosch, et al. “Comparative Analysis of Measures of Viral Reservoirs in HIV-1 Eradication Studies.” PLOS Pathogens 9, no. 2 (February 14, 2013): e1003174. doi:10.1371/journal.ppat.1003174.
34. Ho, Ya-Chi, Liang Shan, Nina N. Hosmane, Jeffrey Wang, Sarah B. Laskey, Daniel I. S. Rosenbloom, Jun Lai, Joel N. Blankson, Janet D. Siliciano, and Robert F. Siliciano. “Replication-Competent Noninduced Proviruses in the Latent Reservoir Increase Barrier to HIV-1 Cure.” Cell 155, no. 3 (October 24, 2013): 540–51. doi:10.1016/j.cell.2013.09.020.
35. Bruner, Katherine M., Alexandra J. Murray, Ross A. Pollack, Mary G. Soliman, Sarah B. Laskey, Adam A. Capoferri, Jun Lai, et al. “Defective Proviruses Rapidly Accumulate during Acute HIV-1 Infection.” Nature Medicine 22, no. 9 (September 2016): 1043–49. doi:10.1038/nm.4156.
36. Hosmane, Nina N., Kyungyoon J. Kwon, Katherine M. Bruner, Adam A. Capoferri, Subul Beg, Daniel I.S. Rosenbloom, Brandon F. Keele, Ya-Chi Ho, Janet D. Siliciano, and Robert F. Siliciano. “Proliferation of Latently Infected CD4+ T Cells Carrying Replication-Competent HIV-1: Potential Role in Latent Reservoir Dynamics.” Journal of Experimental Medicine 214, no. 4 (March 24, 2017): 959–72. doi:10.1084/jem.20170193.
37. Maldarelli, F., X. Wu, L. Su, F. R. Simonetti, W. Shao, S. Hill, J. Spindler, et al. “Specific HIV Integration Sites Are Linked to Clonal Expansion and Persistence of Infected Cells.” Science 345, no. 6193 (July 11, 2014): 179–83. doi:10.1126/science.1254194.
38. Wagner, Thor A., Sherry McLaughlin, Kavita Garg, Charles Y. K. Cheung, Brendan B. Larsen, Sheila Styrchak, Hannah C. Huang, Paul T. Edlefsen, James I. Mullins, and Lisa M. Frenkel. “Proliferation of Cells with HIV Integrated into Cancer Genes Contributes to Persistent Infection.” Science 345, no. 6196 (August 1, 2014): 570–73. doi:10.1126/science.1256304.

Index

• 1.5 John Coffin — The Origin of Molecular Retrovirology
• 2.4 Robert Gallo — Discoveries of Human Retrovirus, Their Linkage to Disease as Causative Agents & Preparation for the Future
• 2.5 Françoise Barré-Sinoussi — Discovery of HIV
• 3.3 Douglas Richman: Antiviral Drug Resistance and Combination ART
• 3.5 Daria Hazuda: Discovery and Development of Integrase Inhibitors
• 3.6 John C. Martin — Making it Simpler: A Single Pill to Treat HIV
• 4.0.1 Jeffrey Lifson — Session 4, Introduction 1
• 4.0.2 Ruth Ruprecht — Session 4, Introduction 2
• 5.1 Flossie Wong-Staal — Discovery of Human Retroviral Transactivators
• 5.5 Andrew Rice — Mechanism of tat Transactivation
• 6.2 Dennis Burton — How Does HIV Evade the Antibody Response?
• 6.3 Bruce Walker — Role of T Cells in Controlling HIV Infection
• 8.1 John Mellors — MACS and Beyond: Epidemiology, Viremia and Pathogenesis
• 8.2 David Ho — Unraveling of HIV Dynamics In Vivo
• 8.5 Sharon Lewin — Research to a Cure: A Possible Goal?
• 8.6 David Baltimore — Bringing it to an End (And Where Are We Going?)
• amfAR
• antiretroviral therapy (ART)
• APOBEC
• Berlin patient, Timothy Ray Brown (1966–2020)
• blood — banks, donors, plasma, screening, transfusions, clotting factors (factor VIII), PBMCs
• capsid, capsid protein (p24)
• CCR5 (chemokine receptor type 5)
• cell culture, tissue culture, immortalized cell line
• cytokines
• Deeks, Steven
• dose response
• drug resistance
• Duesberg, Peter H. (b. 1936)
• env
• enzyme-linked immunosorbent assay (ELISA)
• Finzi, Diana
• Frenkel, Lisa M.
  scientific competition and collaboration
• hematopoietic stem cell transplantation (HSCT)
• Henrich, Timothy J.
• hepatitis
• Hughes, Stephen H.
• hypothesis
• integrase inhibitors
• interleukins
• International AIDS Society (IAS)
• Johns Hopkins University, Johns Hopkins University School of Medicine
• Keele, Brandon F.
• Lane, H. Clifford
  limiting dilution
• LTR (long terminal repeat)
• Maldarelli, Frank
• Margolis, David M.
• Martin Delaney Collaboratory
• models (model systems, model organisms, modeling)
  quantitative viral outgrowth assay (Q-VOA)
• National Institutes of Health (NIH)
• natural selection, evolutionary selection, evolutionary fitness
• Nature (journal)
• NF-κB
• PCR (polymerase chain reaction)
• Persaud, Deborah
• protease inhibitors
• provirus
• reproducibility; experimental reproduction
• reverse transcriptase
• sequencing
• Session 10: What Have We Learned?
• Session 5: Molecular Biology of the Extraordinary Virus
• Session 8: Pathogenesis and Prospects
• sheep
• Shen, Lin
• simian immunodeficiency virus (SIV)
• Stevenson, Mario
• valproic acid
• viral reservoir, viral latency, disease reservoir
• viremia
• Visna-maedi virus (VMV)