Mystery Rays from Outer Space

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

March 31st, 2009

Baffling vaccine quiz

It’s a busy day today as I submit a grant application, so here’s a quick quiz.  Based on the following charts, can anyone guess the years in which vaccination against measles, mumps, and rubella was introduced to the US? Click for larger versions, should you need it.

Measles cases and deaths

Mumps cases

Rubella cases

Pretty tricky, eh?

March 27th, 2009

On diversity in rhinoviruses

Human rhinoviruses (HRV) are tiny, highly variable viruses that are one of the main causes of the common cold.   Stephen Liggett’s group has analyzed all 99 human rhinovirus genomes in the ATCC and come up with all kinds of fascinating insights. 1

How diverse are HRV? What maintains diversity or  lack of diversity?

The lack of broader diversity suggests all HRVs are in a stable status for maintaining selection for certain traits, yet still have mutational flexibility for escape from immune responses.

Have we found most of the HRV out there?

… the sequence space occupied by the available samples suggest that there may be many additional HRV-C strains awaiting discovery. Distance extrapolations relative to the new full reference cohort, predict the HRV-C may have an even broader range of serotypes than the original 99, of which each confers only limited immunologic cross-protection to another.

Where do new HRV come from?

Co-infection with multiple HRVs is known to occur, and we now know this can lead to unique strains that may have distinct biologic properties and clinical characteristics.

Here’s the big picture (click for a larger version).

Liggett human rhinoviruses

Update: Vincent Racaniello of This Week in Virology and The Virology Blog notes in the comments that the ATCC sequences this paper relies on understate rhinovirus diversity, at least partly because an unknown number of rhinoviruses can’t be cultured for classical identification, and points out a paper from last year2 that identified other pathogenic human rhinovirus by a sequencing approach.


  1. Palmenberg, A., Spiro, D., Kuzmickas, R., Wang, S., Djikeng, A., Rathe, J., Fraser-Liggett, C., & Liggett, S. (2009). Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveals Structure and Evolution Science DOI: 10.1126/science.1165557 []
  2. DOMINGUEZ, S., BRIESE, T., PALACIOS, G., HUI, J., VILLARI, J., KAPOOR, V., TOKARZ, R., GLODE, M., ANDERSON, M., & ROBINSON, C. (2008). Multiplex MassTag-PCR for respiratory pathogens in pediatric nasopharyngeal washes negative by conventional diagnostic testing shows a high prevalence of viruses belonging to a newly recognized rhinovirus clade Journal of Clinical Virology, 43 (2), 219-222 DOI: 10.1016/j.jcv.2008.06.007[]
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[]
March 23rd, 2009

Controlling cancer by blocking exhaustion?

Melanoma antigens
Melanoma antigens

The other day I talked about about resurrecting the antiviral response in HIV patients. 1 Antiviral T cells in HIV (and other chronic immune responses) become exhausted: After long exposure to antigen, the cytotoxic T lymphocytes (CTL) become dysfunctional, incapable of mounting a potent response to the virus. This exhausted state is correlated with a number of surface flags, especially the molecules PD-1 and CTLA-4. These aren’t merely flags, but rather they actually transmit the signal to become exhausted.  So it turns out that blocking PD-1 reversed the exhaustion, restored  CTL to their youthful vigor, and allowed them to effectively suppress the virus replication. All the monkeys treated with PD-1 blockade survived, whereas most of those left untreated died within a few months.

As I say, exhaustion isn’t unique to HIV. Probably any chronic exposure to antigen tends to cause  T cell inhibition. There’s molecular logic behind this; if you’ve been fighting an infection for many months, you’re probably not winning, and your immune response is probably doing as much damage as the infection would. Or — even worse — you’re not fighting an infection at all, you’re attacking yourself (because of course you can’t eliminate your own antigens). So maybe it’s time to back off a few notches on the attack and try to reach an accommodation with the antigen.

There are a number of cases — probably many cases — where this seems to work well. Rodents that are chronically infected with hantaviruses turn on a regulatory T cell (TReg) type response, shutting own the attack on the virus and letting them become persistent infections. This comes with some cost, but not too much; probably the infected rodents do much better by letting the virus persist, than if they kept trying to fight the infection.

TRegs
TRegs in skin

There’s another condition when T cells chronically attempt to attack foreign antigen, frequently fail to eliminate it, and become inhibited. This is, of course, cancer. The nature of the CTL inhibition may not be exactly the same as in HIV infections and other CTL exhaustion scenarios, but it’s pretty clear that in general, CTL are not very effective against tumors. After all, most tumors don’t spontaneously regress after a few weeks.

This is probably because when CTL are effective against tumors, that tumor never becomes detectable. In other words, we are only aware of those cancer where CTL are ineffective. (See here (part I) and here (part II) for more detail.) What often happens with tumors, that may be less of an issue with virus infections, is that TRegs become activated and move into the tumor; TRegs shut down aggressive immune responses. As a result, even if you infuse the patient with active anti-tumor cells, or vaccinate and activate the anti-tumor response that way, the anti-tumor response is often quickly shut down by the TRegs and the response never really goes very far.

So can the ineffective T cell response in tumors be reversed, as was done with the ineffective T cell response in SIV? It certainly can — but, as with most anti-tumor immune therapies, it doesn’t work all the time.

With tumors, unlike virus-associated exhaustion, the CTL dysfunction seems to be often associated with the CTLA-4 cell marker. As with PD-1, CTLA-4 isn’t just a marker, it transmits signals into the T cell and actively drives the cells into an inhibited state. (CTLA-4 is probably part of the TReg arsenal, though not the whole of it.) So blocking CTLA-4 in tumor patients has been of intense interest for quite a long time — I think Jim Allison first tried it well over a decade ago2. In general the results have been encouraging, but unspectacular. (It seems that immune treatment of cancer is always encouraging but unspectacular. The problem has been to get consistent effectiveness, rather than occasional amazing cures.)

Melanoma blood vessel
Melanoma blood vessel

This isn’t a safe and innocuous treatment. CTLA-4 is part of the normal immune regulation machinery, and given that, it’s not surprising that CTLA-4 blockade often leads to autoimmunity. In fact, it seems that the more effective the anti-tumor effect is, the more likely the patient is to develop autoimmunity – sometimes quite severe. Compare this to the PD-1 blockade in monkeys, where there wasn’t much autoimmunity, if any.  (Incidentally, before the PD-1 blockade that seemed to work, CTLA-4 blockade has been tried in SIV-infected monkeys.  It didn’t seem to do much.)

A recent paper3 has connected CTLA-4 blockade to the emerging theme of polyfunctionality. As I’ve noted before, it’s become clear over the past couple of years that not all CTL are equal. In HIV infection, polyfunctional CTL — CTL that are capable of producing a wide range of effects, rather than just one or two — are often linked to suppression of the virus. In melanoma patients treated with CTLA-4 blockade, not only were more T cells specific for melanoma antigens present, but those CTL were more likely to be polyfunctional — thus more likely to be effective at destroying the tumor — and those patients were much more likely to have regression of their tumors than in people without CTLA-4 blockade.

So the concept that TRegs — or some other inhibitory effect associated with CTLA-4 — suppress anti-tumor immune responses is likely to be correct, and it seems that at least in some cases it’s possible to override that inhibition and drive T cells to once again attack the tumor effectively. When that happens, cancer can be cured. It’s just a question of being able to do this on a consistent basis. Unfortunately, that’s still the hard part.


  1. The actual experiment was done in SIV infected macaques, but of course the hope is that it will translate to the human virus as well.
    []
  2. Enhancement of antitumor immunity by CTLA-4 blockade. Leach DR, Krummel MF, Allison JP. Science. 1996 Mar 22;271(5256):1734-6.
    []
  3. Yuan, J., Gnjatic, S., Li, H., Powel, S., Gallardo, H., Ritter, E., Ku, G., Jungbluth, A., Segal, N., Rasalan, T., Manukian, G., Xu, Y., Roman, R., Terzulli, S., Heywood, M., Pogoriler, E., Ritter, G., Old, L., Allison, J., & Wolchok, J. (2008). CTLA-4 blockade enhances polyfunctional NY-ESO-1 specific T cell responses in metastatic melanoma patients with clinical benefit Proceedings of the National Academy of Sciences, 105 (51), 20410-20415 DOI: 10.1073/pnas.0810114105
    []
March 20th, 2009

Software I like

Evernote example
This is searchable text in Evernote

It’s not like I have much influence, but I want to give a quick shout out to three pieces of software that I’m finding useful in the lab: DokuWiki, Evernote, and Dropbox.

Dokuwiki, I’ve mentioned before; I use it as my electronic lab notebook.  It has all the standard Wiki features – easy lnks, images and text — with the major advantage over several other wikis that the pages are essentially stored as plain text, making backups, searches, and futureproofing relatively easy. A little rsync magic means that the version on my laptop is auto-synced to a remote copy for backup.

Evernote is a note-storage service.  It has a web interface and desktop apps for Mac and Windows, as well as iPhone integration, and it has useful gimimicks like OCR that can make handwriting  searchable text.  The iPhone integration is what turned this from a mildly useful service to one I use every day.  All the scribbled notes I make to myself in the lab, I now take snapshots of; they’re dumped into Evernote, and then when I write up the experiment, or when I’m replicating it, I have exactly what I did at my fingertips.  And for things that otherwise take a thousand words (like the number of colonies I get from a transformation of a particular ligation), a photo can be a better explanation.  Dump the photo into Dokuwiki, and  I don’t have to wonder if “LOTS OF COLONIES” means a hundred, or what.

Evernote example
More searchable text

Dropbox is file sharing.  Put a dropbox folder on your computer, and anything you put in that folder is silently and promptly synced to any other computer you use — Mac, Windows, Linux.   Even more usefully, symlinks work; take any folders you’re working on, and put symlinks to them in Dropbox, and forget about anything else.  Any time you work on a file or add anything new, the changes are intantly synced and made available on all the other machines. There’s no iPhone client, yet, but iStorage and similar iPhone apps work beautifully with it; so I essentially have my entire computer in my pocket all the time.

But that’s not what makes it so useful in the lab.  It also allows folders to be shared between different people.  That means that for relatively large files and folders (flow cytometry runs in the 100 MB range, confocal experiments that are two or three times that) my students and tech don’t have to fuss with compression and emails and hunting me down with flash drives or whatever.  Just drop the experiment in the shared Lab Folder on any of the computers, and a moment later it silently appears on my laptop.  My collaborator in Greece and I are editing a grant application; it’s in our shared dropbox folder, and whenever he makes changes they’re instantly reflected on my machine, and vice versa.

All three of these are freeware, though Evernote and Dropbox have paid versions with higher capacity.  I haven’t needed them yet, but probably will eventually, and they make my life easy enough that I’ll be happy to shell out for them.

March 19th, 2009

On systemic immunity in flies

Saleh et al Fig 3

It was previously thought that Drosophila is unable to spread systemically an RNAi response, based on observations that endogenously expressed RNA hairpins do not spread from cell to cell. However, we demonstrate that, upon virus infection, infected cells spread systemically a silencing signal that elicits protective RNAi-dependent immunity throughout the organism. … In striking parallel to vertebrates, flies also rely on systemic immunity, albeit in this case the virus-specific signal is dsRNA-based. 1


  1. Saleh, M., Tassetto, M., van Rij, R., Goic, B., Gausson, V., Berry, B., Jacquier, C., Antoniewski, C., & Andino, R. (2009). Antiviral immunity in Drosophila requires systemic RNA interference spread Nature, 458 (7236), 346-350 DOI: 10.1038/nature07712[]
March 16th, 2009

Controlling HIV by blocking exhaustion

HIV modelThe immune system needs to be rigorously controlled, lest it break its banks and flood the body with destructive responses. Any immune stimulant carries its own brakes; a response to an antigen peaks and then crashes as fast as it accelerated. When the brakes fail, autoimmunity and immune-mediated damage can be more lethal than the pathogen.

This gets complicated with chronic infections. Is it better to shut down the immune response, and let the pathogen romp through your body unchecked, or to let the immune response continue, and risk autoimmune disease? In some cases, shutting down the immune response seems to work pretty well; rodents infected with Hantaviruses (see here, for example) don’t try to fight off these viruses very aggressively, and tolerate the persistent infection pretty well (though not perfectly).

In other cases, though, reducing the immune response may be harmful. Hepatitis C virus infection in humans is linked to high TReg levels and to reduced immune response, and that may be one reason why it persists.

(By the way, it’s worth spelling out what I mean by “reducing the immune response”. In many cases this is mainly a regulatory T cell (TReg) effect, meaning it’s actually an active suppression of the aggressive immune response. Saying that the immune response is “reduced” or “shut down” really isn’t accurate; there’s still a strong and specific immune response, it’s just that the response has been redirected from attacking the pathogen, to controlling the anti-pathogen response. But it’s easier to say that it’s reduced.)

What category is HIV in? Is disease linked to an overactive immune response, or would cranking up immunity suppress the virus and reduce disease?  It’s been unclear, but the consensus is gradually tipping to the idea that the TReg response in HIV infection is more harmful overall (see this paper1 and the commentary from the Treatment Action Group blog, for example). A recent paper2 from the Emory Vaccine Center in Atlanta answers this more directly for SIV in macaques, which may or may not be a valid model for HIV in humans.

Sleeping Salaryman
“Exhausted Salaryman” – Hiromy

Cytotoxic T lymphocytes (the antiviral killer cells) in chronic viral infections often are “exhausted”: After a certain period of attack, the CTL become dysfunctional, or at least have reduced function. (I believe, but do not know for sure, that this is related to the concept of “polyfunctional” CTL that has recently become popular — control of HIV is correlated with CTL that can produce many different antiviral reagents, while uncontrolled HIV is correlated with CTL that only have one or a few of these reagents. See this post for a little more on that.) This “exhaustion” concept is relatively new, and it’s only in the past couple of years that physical markers of exhaustion have been identified. One such marker is the PD-1 (Programmed-Death-1) molecule,3 and in fact PD-1 is upregulated on CTL during HIV infection.4

PD-1 is not a mere passive flag. It’s a receptor that actively drives cells into an inhibited state. If PD-1 is the major reason that CTL are dysfunctional in HIV infection, then perhaps suppressing PD-1 will regenerate the immune response and shut down HIV. Or, of course, it could crank up all the immune responses including those you want shut down, and could lead to a massive and fatal autoimmune attack.

With the SIV/macaque model — amazingly enough; there hasn’t been a lot of good news on the HIV front for a while — blocking PD-1 actually worked just as you’d want it to. After blocking PD-1, anti-SIV CTL frequency roared up,  doubling the pre-treatment levels within a couple of weeks.

After PD-1 blockade, the Gag-CM9 tetramer-specific CD8 T cells expanded rapidly and peaked by 7-21 days. At the peak response, these levels were about 2.5-11-fold higher than their respective levels on day 0.2

Velu et al, Fig 4e: Survival curveAnd these newly abundant CTL were polyfunctional; they were far more likely to express multiple cytokines than the CTL pre-treatment. Remembering that polyfunctional CTL are correlated with control of HIV, it wasn’t so surprising that after PD-1 treatment SIV levels dropped dramatically after treatment as well. Most impressively, all the treated monkeys survived for at least 150 days, while 4 of the 5 control-treated macaques had died by then (see the survival curve to the left here).

Critically, the PD-1 treatment didn’t cause any side-effects in these monkeys, so at least over this relatively short period autoimmunity wasn’t a problem. Of course, HIV in humans is not exactly like SIV in macaques, and if it turned out to be necessary to have long-term treatment it may be a different story. Even if autoimmunity doesn’t develop, we think that having too many activated CD4 T cells (as opposed to CD8 T cells, CTL) is a bad thing for HIV patients because it makes the CD4 cells more susceptible to infection; if blocking PD-1 increases CD4 activation it might end up being harmful after all.   On the third hand5 it’s conceivable that a short-term treatment might reverse the exhaustion and allow the immune system to control HIV, with no further help, for a long period.

Who knows what’s going to happen when it moves into humans;  but so far at least,  it’s one of the most encouraging anti-HIV findings I’ve seen for quite a while.


  1. Regulatory T Cell Expansion and Immune Activation during Untreated HIV Type 1 Infection Are Associated with Disease Progression. Weiwei Cao, Beth D. Jamieson, Lance E. Hultin, Patricia M. Hultin, and Roger Detels. AIDS Research and Human Retroviruses. February 2009, 25(2): 183-191. doi:10.1089/aid.2008.0140. []
  2. Velu, V., Titanji, K., Zhu, B., Husain, S., Pladevega, A., Lai, L., Vanderford, T., Chennareddi, L., Silvestri, G., Freeman, G., Ahmed, R., & Amara, R. (2008). Enhancing SIV-specific immunity in vivo by PD-1 blockade Nature, 458 (7235), 206-210 DOI: 10.1038/nature07662[][]
  3. Restoring function in exhausted CD8 T cells during chronic viral infection. Barber DL, Wherry EJ, Masopust D, Zhu B, Allison JP, Sharpe AH, Freeman GJ, Ahmed R. Nature. 2006 Feb 9;439(7077):682-7. []
  4. Among several other papers:
    PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression. Day CL, Kaufmann DE, Kiepiela P, Brown JA, Moodley ES, Reddy S, Mackey EW, Miller JD, Leslie AJ, DePierres C, Mncube Z, Duraiswamy J, Zhu B, Eichbaum Q, Altfeld M, Wherry EJ, Coovadia HM, Goulder PJ, Klenerman P, Ahmed R, Freeman GJ, Walker BD. Nature. 2006 Sep 21;443(7109):350-4. []
  5. Abuse of mutagenic drugs is a constant problem among scientists[]
March 12th, 2009

A successful trial of a malaria vaccine

Plasmodium and RBCThe point of a vaccine trial is to test whether the vaccine works.  If you get an answer to that question, the trial is a success.  The answer may be “No”, in which case the vaccine is a failure, but the trial would still be a success.  (The STEP HIV vaccine trial was therefore a success, though the vaccine was a failure.)

Malaria vaccines have been desperately needed forever, and in the past year there have been a few clinical trials. 1  An encouraging, though unspectacular, trial was reported last year, where the vaccine offered modest protection in children. 2

The most successful vaccines seem to be T-cell based, rather than antibody-based, and the latest report, of a Phase II trial in Kenya,3 drives another nail in the antibody/malaria coffin:

The FMP1/AS02 vaccine did not protect children living in Kombewa against first episodes of P. falciparum malaria; it did not reduce the overall incidences of clinical malaria episodes or of malaria infections, and did not reduce parasite densities … Because of the clearly demonstrated overall lack of efficacy in this trial, FMP1/AS02 is no longer a promising candidate for further development as a monovalent malaria vaccine. … We therefore propose that future MSP-142 vaccine development efforts should focus on other antigen constructs and formulations. 3

For more reading about immunity to malaria:


  1. I don’t actually know much about the history of malaria vaccines, as far as trials go, so I don’t know how unusual it is to have clinical trials.  People have been working on malaria vaccines for decades, but none have worked very well.[]
  2. Abdulla, S., Oberholzer, R., Juma, O., Kubhoja, S., Machera, F., Membi, C., Omari, S., Urassa, A., Mshinda, H., Jumanne, A., Salim, N., Shomari, M., Aebi, T., Schellenberg, D. M., Carter, T., Villafana, T., Demoitie, M. A., Dubois, M. C., Leach, A., Lievens, M., Vekemans, J., Cohen, J., Ballou, W. R., and Tanner, M. (2008). Safety and immunogenicity of RTS,S/AS02D malaria vaccine in infants. N. Engl. J. Med. 359, 2533-2544. doi:10.1056/NEJMoa0807773

    Bejon, P., Lusingu, J., Olotu, A., Leach, A., Lievens, M., Vekemans, J., Mshamu, S., Lang, T., Gould, J., Dubois, M. C., Demoitie, M. A., Stallaert, J. F., Vansadia, P., Carter, T., Njuguna, P., Awuondo, K. O., Malabeja, A., Abdul, O., Gesase, S., Mturi, N., Drakeley, C. J., Savarese, B., Villafana, T., Ballou, W. R., Cohen, J., Riley, E. M., Lemnge, M. M., Marsh, K., and von Seidlein, L. (2008). Efficacy of RTS,S/AS01E vaccine against malaria in children 5 to 17 months of age. N. Engl. J. Med. 359, 2521-2532. doi:10.1056/NEJMoa0807381[]

  3. Ogutu, B., Apollo, O., McKinney, D., Okoth, W., Siangla, J., Dubovsky, F., Tucker, K., Waitumbi, J., Diggs, C., Wittes, J., Malkin, E., Leach, A., Soisson, L., Milman, J., Otieno, L., Holland, C., Polhemus, M., Remich, S., Ockenhouse, C., Cohen, J., Ballou, W., Martin, S., Angov, E., Stewart, V., Lyon, J., Heppner, D., Withers, M., & , . (2009). Blood Stage Malaria Vaccine Eliciting High Antigen-Specific Antibody Concentrations Confers No Protection to Young Children in Western Kenya PLoS ONE, 4 (3) DOI: 10.1371/journal.pone.0004708[][]
March 9th, 2009

The next step in the HIV arms race?

Frog & Toad (Arnold Lobel)Any time a species meets some kind of barrier, there’s going to be selection to overcome that barrier.  In the case of pathogens, one major barrier they have to hurdle is their hosts’ immune systems.  What’s more, this isn’t a simple, static barrier.  Immune systems change on a day-to-day basis; and immune systems also change on a population basis, as the individuals in the host population are in turn selected by the pathogen.

Last week I talked about an example where a population — frogs in the UK, in this case — are apparently being selected by a pathogen.   The relatively recent introduction of frog virus 3 into the UK has caused large-scale die-offs of frogs there, and Teacher et al.1 have just shown evidence that the survivors have been selected for a particular MHC class I type.

MHC class I is often associated with resistance to viruses, because it’s responsible for recognition by antiviral T cells.  What probably happens is that viruses sweep through a population, infecting (and imposing a selective pressure on) most members of the population.  A few individuals that happens to have some particular MHC class I type are relatively resistant to the virus, and have a selective advantage; that MHC allele becomes more frequent in the population; and the population as a whole becomes relatively resistant to the virus.  Of course, this now presents a new barrier to the original virus, and there’s selective pressure on it; virus mutants that are resistant to that particular MHC type do better; the virus sweeps through the new population; and a new minority with a different MHC type has a new selective advantage.

This is the most popular model (“frequency-dependent selection”), but it’s been hard to definitively show examples of it because things are happening on a evolutionary timescale. Even with the very rapid (as evolution goes) change in the UK frogs’ MHC, we don’t have all the pieces.  We see that frogs in the UK have a different set of MHC alleles than those frogs that haven’t been exposed to FV3, but we don’t have the population frequencies of these alleles over the time since the virus was introduced.  And we don’t have examples of  the virus accommodating itself to the new MHC; we’d see that as virus sequences changing over time.

Last week I ended the frog story by saying:

Some people may wonder if this frog virus story has any real relevance to humans. Well, apart from the pure scientific interest of tracking a potential frequency-dependent selection event in real time, one of the clearest links between an MHC class I allele and resistance to a viral infection is in humans, where the MHC class I alleles HLA-B27 and HLA-B57 are linked to resistance to HIV and HCV. Is it possible for HIV to adapt at the population level, so that the dominant strains of HIV in the world are no longer contained by HLA-B57? More generally, if we succeed in developing a T cell-based vaccine against HIV, it will probably have strong allele-dependent effects — will HIV adapt to this vaccine?

SeesawAstute readers2 may have guessed that I wasn’t just guessing wildly, and indeed I had already seen the paper from Kawashima et al.,3 on exactly this topic.

Even though HIV is generally incredibly good at ripping through human immune responses without being controlled, there are some people who are long-term non-progressors (LTNP); they’re infected with HIV, yet they manage to control the virus pretty well, without antiviral treatment, for long periods. Many of these people, it turns out, have a particular subset of MHC class I types; they’re much more likely than the general population to have the HLA-B51, HLA-B57, or HLA-B27 MHC class I alleles.

HIV normally mutates very rapidly within infected individuals, so that as an antiviral immune response arises the virus may be temporarily controlled, but the new mutations that arise escape from the immune control and continue to replicate.  It seems that this immune escape is less likely to happen when the individual has one of the LTNP-associated alleles, and that’s probably because the immune target associated with HLA-B51 (etc) is essential for the virus’s survival.  When HIV mutates the immune target, the virus can’t replicate properly.  The only way HIV can escape immune control by people with these MHC alleles is to make multiple mutations at the same time, compensating for the escape mutation with several other changes.  These multiple mutations are exponentially less probable than single mutations, so the virus is essentially controlled, for a long time.

Humans are today a very large, highly mixed population, and it would take a vast plague, even worse than HIV, to rapidly cause frequency changes that we could measure in the brief period since HIV become common.4  But that hasn’t always been true; humans historically have included relatively small and isolated populations subject to intense disease selection, and we believe we see the outcome of that today in that different human populations  have different frequencies of HLA-B51, B57, and B27 — the equivalent of frogs in the UK vs. elsewhere.

What’s happening to HIV in those areas where HLA-B51 is common?  The prediction is that viruses that have managed to make the mutations that give resistance to HLA-B51 should have a selective advantage in those areas that isn’t seen elsewhere.  That’s precisely what Kawashima et al. saw.

… the frequency of these epitope variants (n = 14) was consistently correlated with the prevalence of the restricting HLA allele in the different cohorts (together, P < 0.0001), demonstrating strong evidence of HIV adaptation to HLA at a population level.  3

HLA-B51 + HIV peptide
HLA-B51 complexed with an immunodominant HIV peptide

Immune escape isn’t the only selective pressure on HIV.  There’s the ability to spread from one individual to another, for example, which isn’t necessarily linked to immune escape.  In principle, some of the other selective factors may counteract immune escape selection.  And in general, some (though not all) of the mutations that allow a virus to escape immune control by on individual are harmful to the virus. That means that some of the escape sequences will quickly revert back to the generic HIV sequence. If HLA-B51 is rare in the population, the virus will constantly be reverting back to generic sequences and the HLA-B51-resistant strain will not particularly accumulate.  But if HLA-B51 is common, even these reverting sequences will build up in the population.

As anticipated, non-reverting variants such as I135X accumulate at the population level, but even rapidly reverting mutations such as T242N can accumulate, if the selection rate exceeds the reversion rate 3

Perhaps as a result, formerly-protective MHC alleles are no longer protective in some areas:

Data here suggest that, whereas 25 years ago HLA-B*51 was protective in Japan, this is no longer the case. The apparent increase in I135X5 frequency in Japan over this time supports the notion that HLA-B*51 protection against HIV disease progression hinges on availability of the HLA-B*51-restricted TAFTIPSI6  response. However, whether this is the case remains unknown. 3

Any effective anti-HIV vaccine will probably rely on antiviral T cells, and will therefore rely on MHC class I presentation.  What this paper suggests is that HIV is likely to be a moving target.  Even if an effective vaccine is developed, it is possible that the virus will gradually evolve resistance to the vaccine.

Thus, the data presented here, showing evidence that the virus is adapting to CD8+ T-cell responses, … highlight the dynamic nature of the challenge for an HIV vaccine. … The induction of broad Gag-specific CD8+ T-cell responses may be a successful vaccine strategy, but such a vaccine will be most effective if tailored to the viral sequences prevailing, and thus may need to be modified periodically to keep pace with the evolving virus.  3

Since we still don’t have any vaccine that protects against HIV at all, this is pretty much a hypothetical worry.  Still, it’s something to think about for the future.


  1. Amber G. F. Teacher, Trenton W. J. Garner, Richard A. Nichols (2009). Evidence for Directional Selection at a Novel Major Histocompatibility Class I Marker in Wild Common Frogs (Rana temporaria) Exposed to a Viral Pathogen (Ranavirus) PLoS ONE, 4 (2) DOI: 10.1371/journal.pone.0004616[]
  2. The only kind I have, I’m sure[]
  3. Yuka Kawashima, Katja Pfafferott, John Frater, Philippa Matthews, Rebecca Payne, Marylyn Addo, Hiroyuki Gatanaga, Mamoru Fujiwara, Atsuko Hachiya, Hirokazu Koizumi, Nozomi Kuse, Shinichi Oka, Anna Duda, Andrew Prendergast, Hayley Crawford, Alasdair Leslie, Zabrina Brumme, Chanson Brumme, Todd Allen, Christian Brander, Richard Kaslow, James Tang, Eric Hunter, Susan Allen, Joseph Mulenga, Songee Branch, Tim Roach, Mina John, Simon Mallal, Anthony Ogwu, Roger Shapiro, Julia G. Prado, Sarah Fidler, Jonathan Weber, Oliver G. Pybus, Paul Klenerman, Thumbi Ndung’u, Rodney Phillips, David Heckerman, P. Richard Harrigan, Bruce D. Walker, Masafumi Takiguchi, Philip Goulder (2009). Adaptation of HIV-1 to human leukocyte antigen class I Nature DOI: 10.1038/nature07746[][][][][]
  4. Someone who knows about evolution could probably attach some numbers to this.[]
  5. I135X is the HIV sequence that’s escaped HLA-B51 control[]
  6. TAFTIPSI is the original HIV sequence that’s controlled by HLA-B51[]
March 5th, 2009

On measles vaccination and capitalism

Anti-vaccine loons often claim that the only reason for vaccinations is the capitalist system and the ill-gotten profits of vaccination.

Here’s data1 from that notorious hotbed of capitalism, the People’s Republic of China of 1965, when measles vaccination was introduced.  For Shanghai …

The incidence of morbidity associated with measles ranged from 909 to 3,510/100,000 persons during the period 1953-1965.  From Figure 1 it can be clearly seen that the incidence of morbidity was reduced remarkably after the introduction of mass vaccination and now is maintained at <20/100,000 persons.

Measles in PRC

For other exciting charts:

Note that the Y axis is a log scale, so the precipitous drop in cases from 1965-1967 was from about 2000 to 50 cases per 100,000.  In 1965 the population of the Shanghai area was roughly 10 million,  so a morbidity of 2000/100,000 persons would be roughly 200,000 cases per year. The mortality rate for measles in China (as elsewhere) was around 1-2%,2 so that’s roughly 2000 deaths per year — mainly of infants and children, of course — that the vaccine prevented.

Another typical loon claim is that vaccines don’t actually do anything — it was entirely the improvements in sanitation that happened at the same time. I’d be interested in knowing exactly how Shanghai improved their sanitation by 90% exactly in 1966. And, since the “remarkable” reduction in deaths is amazingly similar to what happened in Finland after the vaccination campaign of 1982, and in Bourkina Fasso after their vaccine campaign of 2002, how coincidentally those countries also introduced new sanitation at exactly the same time as their measles vaccinations.

It would be hard to imagine three more diverse conditions than Finland, Bourkina Fasso, and the People’s Republic of China, but measles vaccination worked equally well in all three.


  1. X. Jianzhi, C. Zhihui (1983). Measles Vaccine in the People’s Republic of China Reviews of Infectious Diseases, 5, 506-510 []
  2. A Review of the Current Impact of Measles in the People’s Republic of China
    Zhang Yihao and Su Wannian
    Reviews of Infectious Diseases, 5:411-416 (1983) []