Mystery Rays from Outer Space

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.

Immune 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[↩]

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:

• HIV and fitness 
  
• HIV mutation
  
• HIV on Mystery Rays

1. ”Long-term non-progressor”[↩]
2. ”Elite suppressor”[↩]

One 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

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[↩]

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.)