Mystery Rays from Outer Space

Meddling with things mankind is not meant to understand. Also, pictures of my kids

March 26th, 2009

HIV escape, one-on-one

Houdini escape - FleischmanIt’s well known that HIV mutates rapidly in infected patients in order to escape from the immune system. The mutations in HIV track with the peptides that bind to MHC class I in any particular patient. When the virus is transmitted to a new patient, though, those mutations don’t help it much, because MHC is so variable between individuals that the new infected person will very likely have a different MHC class I pattern. (In fact, the mutations the virus developed in the first patient, are likely to be actively harmful to the virus.) The virus has to start all over again and discover a new path toward immune escape. Over a long enough time, the virus may be able to slowly accumulate mutations that allow it to escape from the worst of the MHC class I alleles (see here for a possible example), but it’s very difficult, simply because MHC is so diverse.

But MHC class I itself is only the final stage of a longish pathway of antigen presentation — the route by which peptides are produced, modified, transferred into the right location, bind to the right proteins, all that stuff. (If it’s slipped your memory a little, I made a summary page for MHC class I antigen presentation here.) Within that pathway, at least in humans, it’s only the MHC class I heavy chain itself that’s wildly diverse; the other steps are pretty similar between any two individuals. So why doesn’t the virus mutate to avoid one of these monomorphic steps, and then not have to worry about re-mutating all over again after the next transmission?

Putting that less teleologically, why don’t mutations in HIV, that allow it to escape from the monomorphic steps in antigen presentation, persist in each new individual and accumulate within the population? Those mutations should be just as beneficial to the virus in the new infected person as in the original infectee.

Rob de Boer’s group  asked this question recently,1 and found that

… within hosts, proteasome and TAP escape mutations occur frequently. However, on the population level these escapes do not accumulate1

TAP structure - Tampe
TAP structure2

(My emphasis) And the reason is the same reason other immune escape mutations don’t easily accumulate in the population: MHC is too diverse. If I follow the argument correctly, because the other components of the system are monomorphic, they have a very broad specificity for peptides, whereas MHC itself has a fine specificity. The virus can’t mutate every possible sequence in its genome that would interact with, say, TAP, because there would be thousands of them. If a mutation that prevents TAP binding does arise in one host, it’s selected because it prevents recognition of a particular MHC class I-binding peptide, and when it moves into a new host that peptide is no longer relevant for immune escape, so it’s not selected any more.

That means that, even taking the whole antigen presentation pathway into account:

The total number of predicted epitope precursors and CTL epitopes in a large population data set of HIV-1 clade B sequences is not decreasing over time. 1

I am a little cautious about accepting this paper completely, because it’s heavily based on database analysis without a lot of testing; we don’t actually know whether the escape mutations they identify for TAP actually do escape TAP, for example. They make a number of arguments, in passing, for the accuracy of the epitope prediction programs out there; I am slowly backing in to some acceptance of the notion that the predictive programs are getting pretty good, which wasn’t my position a couple of years ago, but I still am not convinced they’re as good as they say here.

But the conclusion is fairly simple and straightforward, and it leads to an interesting suggestion:

… we speculate that only one of the steps in the antigen presentation pathway has to be polymorphic to prevent pathogens from adapting to any step in the pathway. The mechanism functions best when the polymorphy occurs at the most specific step in the pathway, as that increases the fraction of epitope precursors that is not under selection pressure. While in humans it is the MHC class I molecules that are highly polymorphic and specific, other solutions do appear to exist. The TAP molecules of rats are more specific than the human TAP, and have a limited functional polymorphism, and the TAP and MHC genes of chickens are equally polymorphic on the nucleotide level 1

Chicken MHC is an interesting case, and is very strongly linked to resistance to some pathogens. But the reason for the tight linkage to resistance isn’t really known; there’s no obvious reason at the level of the MHC. It might be interesting to look at TAP as part of the resistance, as well.  I have some chicken stuff in the lab, and I should see if we can test that.


  1. Schmid, B., Kesmir, C., & de Boer, R. (2008). The Specificity and Polymorphism of the MHC Class I Prevents the Global Adaptation of HIV-1 to the Monomorphic Proteasome and TAP PLoS ONE, 3 (10) DOI: 10.1371/journal.pone.0003525[][][][]
  2. Structural arrangement of the transmission interface in the antigen ABC transport complex TAP.
    Oancea G, O’Mara ML, Bennett WF, Tieleman DP, Abele R, Tampé R.
    Proc Natl Acad Sci U S A. 2009 Mar 18  doi: 10.1073/pnas.0811260106[]
February 10th, 2009

Immune control of Hepatitis C virus and HIV: coincidence or plan?

HCV and lipid droplets, by Torsten Schaller
HCV protein associated with lipid droplets
Torsten Schaller, Research As Art)

Although there are quite a few viruses that infect and then persist in the infected animal for a long time, most of these viruses don’t cause a lot of problems during the persistent state. Herpesviruses, adenoviruses, and several other families can stick around for a long time (life-long, in the case of most herpesviruses) and although you’ll sometimes see occasional recurrence, and occasionally there can be serious disease from the reactivation (examples being shingles, from recurrent varicella-zoster virus, or the very rare cancers associated with Epstein-Barr virus) — for the most part these are really unusual outcomes. Mostly we can stroll around with our complement of viral passengers and we’re perfectly fine with it.

There are a handful of exceptions, in humans and in other animals, where viruses that cause chronic infection also cause chronic, severe disease. With these viruses we’d like to know why they become chronic in the first place (why doesn’t the immune system eliminate them?), and we’d like to know why they cause disease (why aren’t they like our friendly neighborhood herpesvirus)? We don’t have good answers for either of these questions. In fact, I don’t think we even have a good sense if the answers are the same for different viruses, or whether each of them manages to persist and cause chronic disease through their own unique factors.

Two of the most prominent chronic virus diseases in humans are HIV and HCV (hepatitis C virus). A recent paper1 suggests that these guys may have at least something in common in the way they escape immune control, and in the way the immune system controls them.

HCV protein distribution in cells
HCV protein distribution in infected hepatoma cells
(Mark Harris lab)

It’s pretty well known that one way HIV escapes immune control is that it mutates so fast, the immune system can’t get a grip on it. In particular, the cytotoxic T lymphocytes (CTL) that are specialized to control virus infections need to recognize a stretch of about 9 amino acids (a peptide, in other words), and if that sequence changes the CTL may no longer recognize the virus. (I’ve talked about that here and here.) It’s also become clear that HCV does the same thing, although perhaps less dramatically than does HIV, and that this mutational immune escape is one reason HCV can persist and continue to cause disease (see here for more).

With HIV, there are a number of “elite controllers” who seem to be resistant to the virus’s ability to mutate away from immune control. In many cases this seems to be because the CTL in those individuals are focused on a particular critical stretch of amino acids that simply can’t mutate without severely damaging the virus (reducing HIV’s replicative fitness). The reason these elite controllers select that critical peptide is that they have a MHC class I allele that specifically binds to that peptide sequence. The HLA-B27 and HLA-B57 alleles seem to be particularly likely to find critical peptides, and people with those MHC alleles are more likely to be elite controllers.

The new HCV paper1 shows that HLA-B27 is also protective against HCV infection 2, and for the same reason — the HCV peptide that binds to HLA-B27 is a critical sequence that can’t mutate much without severely damaging the virus. (When HCV does mutate away from HLA-B27-mediated control, it’s because it has developed multiple mutations in the peptide, not just one, and it’s exponentially3 harder for the virus to make two mutations vs. one.)

Is it just a coincidence that HLA-B27 is involved in both cases, or is there something specially magical about HLA-B27? I’d be inclined to say it’s just coincidence except that HLA-B27 is such a special molecule4 already. It’s involved in all kinds of disease risks, both reducing the risk of some infectious diseases like HIV and HCV and dramatically increasing the risk of autoimmune diseases like ankylosing spondylitis and many others. And off the top of my head, I think it’s one of the very ancient and highly diversified groups of HLA molecules. So maybe there is something about it that manages to focus on critical viral peptides, or that makes it a particularly strong stimulator of CTL, and that gives it a selective advantage that outweighs its increased risk of autoimmune disease.


  1. Eva Dazert, Christoph Neumann-Haefelin, Stéphane Bressanelli, Karen Fitzmaurice, Julia Kort, Jörg Timm, Susan McKiernan, Dermot Kelleher, Norbert Gruener, John E. Tavis, Hugo R. Rosen, Jaqueline Shaw, Paul Bowness, Hubert E. Blum, Paul Klenerman, Ralf Bartenschlager, Robert Thimme (2009). Loss of viral fitness and cross-recognition by CD8+ T cells limit HCV escape from a protective HLA-B27–restricted human immune response Journal of Clinical Investigation DOI: 10.1172/JCI36587[][]
  2. This part was already known[]
  3. or maybe geometrically, I don’t know[]
  4. Unicorns have HLA-B27! Well-known fact![]
September 7th, 2008

Viruses, fitness, and unfitness

Hepatitis C virus (HCV)It’s become pretty clear that one way HIV persists in spite of an active, powerful immune response is to mutate its immune targets: “immune escape”.  HIV isn’t the only virus that does this, and we can learn from the others.

Cytotoxic T lymphocytes (CTL) identify virus-infected cells by recognizing short peptides, usually about 9 amino acids long. Each CTL is fairly specific; it only recognizes a single sequence. That means that if even one of the nine amino acids in its target mutates, the CTL is blind to the virus. If the CTL response to a virus is limited to a single peptide (which is, to a first approximation, the most common situation) then this single mutation will allow the virus to escape from the immune system, at least until new CTL arise targeting some different peptide.

The downside of this, from the virus’s viewpoint, is that it doesn’t really “want” to mutate itself. There are a limited number of sequences which allow the virus to replicate and spread efficiently, and to the extent that the mutations drive the virus away from these fairly optimal sequences, the virus is less “fit”. That means that the immune response can actually limit the virus’s replication even after (in fact, because) the virus has mutated away from CTL recognition.

What are the conditions under which this sort of continual partial control and constant escape can take place? One fairly obvious point is that the virus must not be eliminated by the immune system. If the first (or even tenth) CTL response to arise gets rid of all the virus from the host, then there’s no more viral immune evasion. I pointed out a parallel instance of this earlier, where poliovirus undergoes mutation in a person, but only when the person has a deficient immune system and can’t completely clear the virus. The virus needs to undergo constant replication over a long period, which makes this less of an issue for things like herpesviruses — they’re long-standing infections, but typically establish a latent infection rather than replicating throughout the infection. It probably would be helpful for the virus to mutate relatively fast, as well — DNA viruses like adenoviruses (which possibly do continue replication in persistent infection) have a relatively low mutation rate compared to RNA viruses like poliovirus or retroviruses like HIV.

Hepatitis C posterImmune escape by hepatitis C virus

There are several lab animal and veterinary examples where something parallel to HIV immune evasion probably takes place (mouse hepatitis virus; perhaps feline infectious peritonitis virus), but the most popular choice for a close parallel to HIV is another human virus, hepatitis C virus (HCV). HCV, like HIV, can establish a chronic infection in immunocompetent people, and continually replicates. It’s been known that HCV mutates over time, and there’s decent evidence that much of this mutation is driven by escape from CTL. The parallels have become stronger with new evidence1 suggesting that virus fitness changes are an important factor in HCV immune evasion, as well, but there’s a twist that I, as least, haven’t seen in HIV.

In these experiments, the authors experimentally infected a chimpanzee with HCV (as with HIV, there are not many good animal models for HCV) and tracked the immune response, and the dominant viral genome sequences, over some seven years. What’s more, the authors then tested those mutant viruses for their ability to replicate, persist, and evade immunity.

As expected, HCV threw out a bunch of mutations, especially in the early stage of infection, and those mutants were not recognized by the immune system. On the other hand (also as predicted, from the work on HIV) these early mutants were not as good at replicating as was the original (immunogenic) virus: They were less fit.

HCV escape variants can be fit

But — and here’s the twist — there were at least three variants that evaded CTL, arising early (3 months, for one variant), or moderately late (10 months; two variants). The one that arose early was clearly less fit.  It didn’t replicate well even when there was no immune system controlling it (that is, in cultured cells in the incubator), and given the chance, it mutated back to the original sequence.

The later ones, though, were not obviously as damaged; they replicated pretty well in cultured cells, and they did not mutate back to the original parent sequence.

What’s more, one of these relatively-fit variants persisted, more or less unchanged, in the infected chimp for years after it arose. (The other variant, though “fit” in culture, was not in the host, because a new immune response arose that targeted that variant.)

So for HCV, CTL escape mutants can arise, and there is not necessarily a loss of fitness associated with the immune evasion. I don’t remember seeing this established with HIV, but it’s quite likely the same thing happens. (Perhaps it’s even been described in the literature and I’ve missed it.) When immune escape variants are fit and healthy viruses, the immune system hasn’t even imposed a fitness cost on the mutation, and the virus isn’t being significantly controlled by the immune response.

It would be nice to understand better where fitness costs arise, which immune responses drive viruses to these un-fit variants, and how to focus the immune response on a vulnerable target.


  1. Luke Uebelhoer, Jin-Hwan Han, Benoit Callendret, Guaniri Mateu, Naglaa H. Shoukry, Holly L. Hanson, Charles M. Rice, Christopher M. Walker, Arash Grakoui, Darius Moradpour (2008). Stable Cytotoxic T Cell Escape Mutation in Hepatitis C Virus Is Linked to Maintenance of Viral Fitness PLoS Pathogens, 4 (9) DOI: 10.1371/journal.ppat.1000143[]
August 6th, 2008

On HIV elite suppressors

Our results suggest that in some cases, the lower replication capacity of HIV-1 isolates in LTNP1 and ES2 may be the result, rather than the cause, of suppressed evolution: a qualitatively superior HIV-1-specific immune response that limits viral replication will prevent evolution toward greater fitness. … we conclude that the immune system of ES9 is controlling viral replication by at least two different mechanisms: there is a direct inhibition of viral replication by polyfunctional HIV-1-specific CD8+ T cells that proliferate in response to autologous viral peptides, and there is selection for and maintenance of escape mutations that have a negative impact on viral fitness. Vaccines that elicit CD8+ T cells with both properties may be very effective at controlling HIV-1 replication.

Transmission of Human Immunodeficiency Virus Type 1 from a Patient Who Developed AIDS to an Elite Suppressor
Justin R. Bailey, Karen O’Connell, Hung-Chih Yang, Yefei Han, Jie Xu,1 Benjamin Jilek, Thomas M. Williams, Stuart C. Ray, Robert F. Siliciano, and Joel N. Blankson
Journal of Virology, August 2008, p. 7395-7410, Vol. 82, No. 15 doi:10.1128/JVI.00800-08

(My emphasis throughout.)

Further reading:


  1. “Long-term non-progressor”[]
  2. “Elite suppressor”[]
July 24th, 2008

HIV and immunodominance, again

HIV modelOne of the reasons HIV can persist in infected people, in spite of a powerful and effective cytotoxic T cell immune response against the virus, is that the virus mutates rapidly. Because CTL each only target a short stretch of the genome (say, 9 amino acids) and a single amino acid change may allow the virus to escape recognition by a particular CTL clone, it may not take long for a viral mutant to arise that is invisible to the dominant CTL population in a particular individual.

It’s been suggested that immunodominance is one of the factors that determines the rate at which HIV can escape from a particular immune response. In a highly immunodominant response, most of the CTL specific for the virus all target a single peptide epitope. If the virus manages to mutate this peptide, it has escaped the bulk of the immune response, and the new mutant virus can explode unchecked (until a new CTL response arises).

On the other hand, if the CTL response isn’t dominated by a single epitope — that is, if the response is broad, targeting many peptides — the virus has to simultaneously mutate several regions of its genome, which is exponentially less probable than single mutations. On the other hand, typically a broad CTL response would have fewer cells attacking each individual epitope, so perhaps the overall control might not be as good during the peak response.

Directly analyzing these questions is a huge task. Identifying CTL epitopes isn’t easy even when there are a few of them; looking at HIV changes isn’t easy even when there’s a concrete starting point; and in an infected patient you would need to track CTL recognition and HIV changes at short intervals, and over a long period; a task even more complicated by all the variables of a massively diverse starting population, replication and fitness issues … just an overwhelming problem.

A paper in PLoS Computational Biology1 tries to model these possibilities.

Organic computer
Organic computer

I don’t feel competent to assess the model here, in any technical way. As with most bench scientists, I suspect, I’m at best cautious, and more often outright skeptical, about computer modeling of biological problems, especially when they’re as complex as these ones. For example, the authors list a dozen parameters they took from various sources — maximal CTL proliferation rate, natural death rate of CD4 cells, and so on. (Not to mention assumptions that aren’t explicit.) Lots of these parameters are offered as single numbers: 0.01 d-1 as the death rate of CD4 target cells. Naturally, each of those numbers would have error bars in the original, and probably weren’t all measured in comparable ways, and so on. I doubt anyone would be much surprised if any of those parameters was off by 50% or more; perhaps much more. Cumulatively, how much error is in there? Or do we count on having all the errors more or less cancel out?

Still (again, probably typical of bench scientists) I’m always intrigued by computer modeling, and I’m willing to accept that modeling might well open up a problem enough to suggest new approaches. Encouragingly, the model here fits observation reasonably well; escape variants pop up intermittently over a couple of years, CTL clones decline as their targets mutate away. The model looks rather similar, in some ways, to the study a couple of years ago on a pair of identical twins infected with HIV. 2

One interesting observation from the model is that escape variants are mostly all present within a couple of years of infection, though they may later reappear as if they are new as CTL pressure varies:

After about two years, the virus population stabilizes as the ‘easy’ escapes have been done, the replicative capacity is partially restored and only few escapes are expected to appear later during infection. … If an escape is found to happen late it does not necessarily mean that it had not been selected earlier during infection

An observation and prediction arising from this is that CTL may actually become more effective later in infection (all other things being equal, of course), as further attempts by the virus to escape bump up against more severe fitness costs for the virus.

Another observation is the effect of immunodominance. A highly immunodominant CTL response results in more escape variants, as predicted by other studies. However, since escape variants are usually less fit than the Platonic essence of HIV, even though there are more cells infected with virus, that virus is less fit; so even a highly immunodominant response may be surprisingly (to me) effective, by forcing the virus into an unfit state.

A higher degree of immunodominance leads to more frequent escape with a reduced control of viral replication but a substantially impaired replicative capacity of the virus.

Presumably (I don’t think the authors of this model addressed this directly) the effectiveness (quantitatively) of an immunodominant response would depend on the fitness cost — in other words, an immunodominant response that could be escaped with only a small loss in fitness would be ineffective, whereas one that forces a big hit in fitness to escape would be effective. That would reflect what we know about the connection between elite suppressors and particular MHC class I alleles associated with immunodominant epitopes.

I’ve been rather unimpressed by highly immunodominant responses to HIV, but if this model is accurate, such responses may not as bad as I thought; though broad responses are probably still more desirable.


  1. Althaus CL, De Boer RJ (2008) Dynamics of Immune Escape during HIV/SIV Infection. PLoS Comput Biol 4(7): e1000103. doi:10.1371/journal.pcbi.1000103[]
  2. Draenert R, Allen T, Liu Y, Wrin T, Chappey C, et al. (2006) Constraints on HIV-1 evolution and immunodominance revealed in monozygotic adult twins infected with the same virus. J Exp Med 203: 529-39[]
May 10th, 2008

On HIV variation

The amount of HIV diversity within a single infected individual can exceed the variability generated over the course of a global influenza epidemic, the latter of which results in the need for a new vaccine each year.

–Walker BD, Burton DR (2008) Toward an AIDS vaccine. Science 320:760-764.

(See my previous posts here and here for more explanation.)

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