Mystery Rays from Outer Space

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

April 27th, 2009

On immunology and malaria

Malaria life cycle
Life cycle of Plasmodium falciparum

“In this article we have attempted to make the case that we may not know enough about malaria to make an effective vaccine. If we agree that the development of a malaria vaccine would profit from a better understanding of the basic immunology of the human response to malaria, we then need to ask the following question: have we engaged a sufficient number of immunologists to address the problem? At the moment, probably not. Relative to the magnitude of the global disease burden imposed by malaria, there are only a small number of scientists with the training and expertise in the human immune system who are committed to working at the molecular interface of the parasite and the immune system.”

Pierce, S., & Miller, L. (2009). World Malaria Day 2009: What Malaria Knows about the Immune System That Immunologists Still Do Not The Journal of Immunology, 182 (9), 5171-5177 DOI: 10.4049/jimmunol.0804153

April 15th, 2009

Malaria vaccination – a victim of its own (feeble) success

Malaria parasites in mosquito midgut
Malaria parasites in mosquito midgut

A followup study 1 of the most successful malaria vaccine to date is not very impressive:

In cohort 2, adjusted efficacy of the RTS,S/AS02A candidate malaria vaccine against first or only clinical malaria episodes in Mozambican children aged 1 to 4 years was of 35.4% during the first six months of follow up (ATP cohort), decreasing to 9.0% in the subsequent 12 months. 1

(My emphasis)  In  the earlier clinical trial, this vaccine had been moderately effective, 2 something like 35-65% efficacy — pretty feeble, but better than other malaria vaccines.  And in one subset of children, the protection seemed to last reasonably well, remaining roughly constant for 21 months. 3   But in this second group of vaccinated children, the protection dropped like a rock.  Why?

The most likely difference is that children in the second (poor long-term protection) group were treated for malaria.  That means the first group was constantly re-exposed to malaria parasites, which acted as a vaccine booster.  The second group didn’t get that booster effect, and their immunity dropped.  (The first group was also in a higher-risk area, again meaning they were more likely to be re-exposed to the parasite.)

Children in cohort 1 were probably exposed to low-density parasitaemias for a longer time than children in cohort 2, in which the development of this enhanced asexual-stage immune response may have been impaired. We propose this may explain a waning of the vaccine-specific protective response in cohort 2. 1

Does this mean the vaccine is useless?  Not at all.  In high-risk areas this can clearly reduce disease.  But equally clearly, this isn’t likely to be helpful for eradicating malaria, because the more successful this vaccine is at reducing malaria, the less effective it will become.


  1. Guinovart, C., Aponte, J., Sacarlal, J., Aide, P., Leach, A., Bassat, Q., Macete, E., Dobaño, C., Lievens, M., Loucq, C., Ballou, W., Cohen, J., & Alonso, P. (2009). Insights into Long-Lasting Protection Induced by RTS,S/AS02A Malaria Vaccine: Further Results from a Phase IIb Trial in Mozambican Children PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005165[][][]
  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. Alonso PL, Sacarlal J, Aponte JJ, Leach A, Macete E, et al. (2005) Duration of protection with RTS,S/AS02A malaria vaccine in prevention of Plasmodium falciparum disease in Mozambican children: single-blind extended follow-up of a randomised controlled trial. Lancet 366: 2012–2018[]
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[][]
February 5th, 2009

Now I really, really like Bill Gates

MosquitoFrom MSNBC:

“Bill Gates just released mosquitos into the audience at TED and said, ‘Not only poor people should experience this.’”

That was the post by Facebook’s Senior Platform Manager Dave Morin on social networking site Twitter.

The event took place at the TED2009 (Technology, Entertainment and Design) conference on Wednesday in Long Beach, Calif., where the Microsoft chairman was delivering a presentation about malaria education and eradication. Malaria is transmitted from person to person via mosquito bites.

The mosquito incident was confirmed by the media office of the Bill and Melinda Gates Foundation, which also noted that the insects released were not carrying malaria. 

Alternate titles:
“It’s a feature, not a bug”
“A patch for Yellow Fever and Dengue will be released with Service Pack 3″

(With thanks to Len Berlind)

July 20th, 2008

Quantity vs quality again

PlasmodiumAll you want in a vaccine is that (1) it doesn’t do any harm, and (2) it prevents disease. When you’re running initial tests on a potential vaccine, though, you often can’t actually include (2) in the tests — especially for a human vaccine– because it’s rarely acceptable to infect your volunteers with, say, HIV. Instead, you identify surrogate measures like level of antibody, or number of T cells, and you judge your vaccine on those surrogate measures at first. If your vaccine doesn’t induce a lot of antibody, say, cytotoxic T lymphocytes (CTL), or whatever it is that you’re measuring, then back to the drawing board.

The problem with that approach, of course, is that we still don’t understand the immune system all that well, and so the surrogate measures that get used may not be ideal. We’ve been seeing this with a number of HIV vaccines, which in preliminary tests induced great surrogate measures but ended up not protecting against disease. This (among other things) has led to a recent focus of quality of immune responses as well as quantity. A recent paper emphasizes this, coming at the issue from a very different direction.

Malaria vaccines haved been a huge challenge to develop. Getting strong immune responses against protective antigens has been pretty difficult, and then moving these into clinical settings has usually shown rather underwhelming efficacy. One of the approaches that was tested, as a way of safely inducing immune responses, was genetic immunization (or DNA vaccines). In this approach, rather than a protein antigen, you inject your patients with DNA encoding the antigen of interest. The DNA gets taken up by cells, expresses your antigen of interest, and hopefully that antigen then induces an immune response.

As I understand it, this approach has worked pretty well in mice, but not so well in humans. Immune responses in humans vaccinated with DNA have usually been very low; so low that (based on these surrogate measures) the vaccines were abandoned and people weren’t challenged with the pathogen.

… it became clear that, for reasons that remain poorly understood, the same high immunogenicity could not be reproduced in humans.. Genetic immunisation of volunteers could induce at best CTL cells but low, or absent, CD4 T-cell and antibody responses. The immunogenicity was so low that, although reported, several clinical trials were considered unsuitable for publication. In many of these trials, challenge by the infectious pathogens was either not possible or decided against in view of the limited responses induced.1

Plasmodium & red blood cellsPierre Druilhe, at the Pasteur institute, decided to test the approach more directly, with a challenge experiment.1 They vaccinated some chimps with a DNA vaccine against a malaria antigen, an approach that had previously led to very weak immune responses in humans. Here again, the immune responses were not very exciting: there was no humoral (antibody) response, though there were detectable MHC class I and MHC class II-restricted T cell responses. But the effect on malaria infection was dramatic; there was 
sterilizing immunity, no detectable parasites, in 3 of the 4 chimps.

The authors comment “these findings suggest that the relative scarcity of an immune response should not necessarily exclude the assessment of the protective efficacy of a vaccine candidate when ethically feasible,” which is a reasonable suggestion, though I think their data don’t really show that this was a “scarce” immune response. Did they really see a low response when you consider T cells, or is it actually a strong response that is strictly biased to the cell-mediated immune response? They didn’t include some information that I’d consider critical — how the T cell responses here compared to a more conventional vaccine approach. They cite an earlier paper2 showing some protection against schistosomiasis in cattle after a DNA vaccine in spite of undetectable antibody responses, to argue that DNA vaccine protecting in spite of a low immune response may be a general effect; but since the schistosomiasis study didn’t even look at T cell responses as far as I can see, it doesn’t answer that question either.

Overall, I think this is not a very strong paper. It’s just a handful of animals (and some of their stats are highly questionable; I don’t think you can challenge 4 animals twice and call that a cumulative N=8), and they don’t show me how the T cell responses compare to other approaches, so I don’t know if it’s even a “weak” immune response. Still, it’s an interesting observation, and emphasizes that it’s important to understand the quality of an immune response as well as quantity.


  1. Daubersies P, Ollomo B, Sauzet J-P, Brahimi K, Perlaza B-L, et al. (2008) Genetic Immunisation by Liver Stage Antigen 3 Protects Chimpanzees against Malaria despite Low Immune Responses. PLoS ONE 3(7): e2659. doi:10.1371/journal.pone.0002659[][]
  2. Field testing of Schistosoma japonicum DNA vaccines in cattle in China. Shi F, Zhang Y, Lin J, Zuo X, Shen W, Cai Y, Ye P, Bickle QD, Taylor MG. Vaccine. 2002 Nov 1;20(31-32):3629-31. []
May 15th, 2008

On parasite/host interactions

I don’t know why I read the ScienceDaily newsfeed, because it drives me crazy every single day.  I had naively thought that whoever massages the press releases they receive would have, maybe, a teeny tiny clue about what’s gone on in the field before, but they seem to have the historic awareness of tree squirrels. Today’s gem:

It’s a paradox that has confounded evolutionary biologists since Charles Darwin published On the Origin of Species in 1859: Since parasites depend on their hosts for survival, why do they harm them? … The study, published in the early online edition of the journal Proceedings of the National Academy of Sciences, provides the first empirical evidence in a natural system of what’s called the trade-off hypothesis.

It’s not a “paradox” at all, and while it may “baffle” the marketing department that wrote the press release ScienceDaily regurgitated, it certainly hasn’t baffled evolutionary biologists for a long time.  I’ve talked about this exact subject here:

… if there’s a link between increased transmission and increased virulence, then the balance will not favour the pathogen becoming benign.

Here:

I’ve previously talked about the common misconception that viruses evolve toward benignity. This is usually phrased something like, “Natural selection favours viruses with low pathogenicity/virulence (so they don’t eradicate their hosts)“, or “Viral pathogenesis is an abnormal situation of no value to the virus”. This claim is clearly wrong –clearly both through common sense, and through observation.

And here:

I’ve observed before that the common belief that viruses evolve toward avirulence is not particularly true. It’s more accurate to say that viruses evolve toward improved transmission. Some viruses are better transmitted if they let their host survive longer, but other viruses have to be virulent in order to spread. The former may evolve toward reduced (though not necessarily loss of) virulence, but the latter would “want” to maintain stable virulence.

December 16th, 2007

Malaria eradication: The smallpox precedent

Tametomo's force driving away the gods of smallpox. Yoshitoshi Taiso, 1890
Tametomo’s force driving away the gods of smallpox. Yoshitoshi Taiso, 1890

Following up to my last post , about the Gates Foundation’s call to eradicate malaria, I thought I would talk about historical experience with eradication of infectious diseases. Here is the list of diseases that have been eradicated throughout all of recorded history:

  1. Smallpox

I’ll pause so you can write that down.

OK, there are a couple of other diseases that are, hopefully, on their way to eradication (notably poliovirus), and there are a bunch of others whose incidence has been spectacularly reduced through vaccination (such as measles, diphtheria, and rubella),1 sanitation (such as guinea worm), and even antibiotics (leprosy). But only smallpox has been eradicated. 2

Why was smallpox eradicated, where four other global eradication campaigns3 failed? What was special about smallpox and its vaccine? What are the factors that allowed this disease to be reduced from millions of cases per year, to none? And, most to the point, what aspects of smallpox eradication are applicable to malaria?

In fact, most of the special aspects of smallpox that allowed it to be eradicated are not particularly true for malaria. Smallpox …

  • Has no animal host. If you can eradicate the disease in humans, it won’t re-emerge from a mouse, or monkey, or bat reservoir — compare to yellow fever, for example.
  • Has no persistent phase. Smallpox either kills people, or they recover completely and eliminate the virus. In either case, if there are no clinical cases over a reasonable period, then you can be confident that there is no more virus.
  • Induces long-term immunity in survivors.
  • Was a fearful enough disease that the political will to eradicate it lasted through the campaign. Smallpox vaccination continued throughout civil wars and other upheavals.
 Vaccinating the poor / Drawn by Sol Ettinge, Jun. 1872
Vaccinating the poor. Sol Ettinge, Jr., 1872

And the smallpox vaccine (vaccinia virus) is also exceptional in that it …

  • Induces very long-term immunity with a single dose. Vaccinia virus induces a memory, and probably protective, immune response for an extraordinarily long time — response have been shown for up to 60 years.
  • Is relatively stable and easy to transport and deliver. With large-scale vaccination campaigns, logistics become the limiting factor, especially as the campaign progresses and the final reservoirs of disease may be in remote, third-world areas.
  • Leaves a marker of treatment. Vaccinated people usually had a small scar at the site of scarification, so that it was possible to identify susceptible people and protect them.

The smallpox vaccine is also exceptional in its frequency and severity of adverse effects. I think that for no disease today would the risks of smallpox vaccine be tolerated — back to the fourth point above, that smallpox was such a terrible disease that people were willing to take the risks of vaccination. 4

There were also a vast number of technical and logistic components that, I think, are mostly applicable to any eradication program (for example, the cost per dose of a vaccine is much less if the vaccine can be prepared in large, multi-dose vials; but that means you need to use the vial up all at once, which means in turn organizing large numbers of vaccination on a single day; and that in turn implies an efficient communication network and so on), and which I won’t talk about here. There’s a fascinating review in Henderson, D. A. (1987). Principles and lessons from the smallpox eradication programme. Bull World Health Organ, 65(4), 535-546. if you want to learn more.

“A much greater change — not apparent but real — was produced by the introduction of vaccination in 1798. It was computed, that, in 1795, when the population of the British Isles was 15,000,000, the deaths produced by the small-pox amounted to 36,000, or nearly 11 per cent. of the whole annual mortality. Now, since not more than one case in 330 terminates fatally under the cow-pox system, either directly by the primary infection, or from the other diseases supervening; the whole of the young persons destroyed by the small-pox might be considered as saved, were vaccination universal, and always properly performed. This is not precisely the case, but one or one and a half per cent. will cover the deficiencies; and we therefore conclude, that vaccination has diminished the annual mortality fully nine per cent. After we had arrived at this conclusion by the process described, we found it confirmed by the authority of Mr Milne, who estimates, in a note to one of his tables, that the mortality of 1 in 40 would be diminished to 1 in 43-45, by exterminating the small-pox. Now this is almost precisely 9 per cent.”
Combe, George. 1847. The Constitution of Man and Its Relation to External Objects. Edinburgh: Maclachlan, Stewart, & Co., Longman & Co.; Simpkin, Marshall, & Co., W. S. Orr & Co., London, James M’Glashan, Dublin.
It’s important to point out that eradication of a disease is possible when not all of these factors are matched — poliovirus, which is almost eradicated (and could have been eradicated altogether with a bit more political help) is different in several ways. But it does offer a checklist for known success. How does malaria match up?

Not so well, actually. Malaria …

  • May have an animal reservoir. Apes can be infected experimentally, and are sometimes naturally infected. This is not a practical issue today, where the animal reservoir is negligible, but if human infection is reduced an animal reservoir might serve as a source for reinfection.
  • Does have a persistent phase. This is especially a concern since partially-immune people (common in endemic areas) can be infected and trasmit the disease without showing clinical symptoms — again, a potential reservoir of re-infection.
  • Does not consistently induce protective immunity.
  • Is a terrible scourge, but one to which the world has become accustomed. Is there the will to take on the cost of eradication? The last attempt at malaria eradication — which failed — cost a billion dollars. As Melinda Gates pointed out, the cost of the disease in perpetuity is greater than the cost of eradication, but the costs come from different places.

Since there are no effective malaria vaccines as yet, we can’t very well compare them to the smallpox vaccine. I don’t know enough about the irradiated vaccine that will enter trials next year, but the “RTS,S/AS02D” vaccine in phase I/II trials5 requires multiple doses and apparently offers relatively low protection — certainly better than nothing, if this holds true through phase III trials, but it’s hard to imagine that it’s sufficient for eradication.

So vaccines are probably going to be an important component of malaria eradication (if it happens) but the nature of the disease means that they’re not likely to be sufficient. Melinda Gates said in her eradication speech that “This is a long-term goal; it will not come soon,” and she focused on four “intervention points”:

To eradicate malaria, you have to end transmission — and there are multiple points where you can intervene. Reduce the number of infected mosquitoes. Keep mosquitoes from biting people. Keep people who are bitten from getting infected. Keep people who are infected from transmitting malaria back to mosquitoes.

Vaccines are good candidates to help with the last two points, and may help with the first. But overall, this is a more complex problem than smallpox. Nevertheless, smallpox eradication has plenty of lessons for malaria, as well.


  1. A great review, with dramatic incidence tables is: Roush, S. W. & Murphy, T. V. (2007). Historical comparisons of morbidity and mortality for vaccine-preventable diseases in the United States. JAMA, 298(18), 2155-2163. I have adapted their numbers to make a table here []
  2. It is probably true that there are stocks of the virus around as well as the official stocks. However, there have been no cases of “wild” human smallpox since 1977.[]
  3. Henderson, D. A. (1999). Lessons from the eradication campaigns. Vaccine, 17 Suppl 3, S53-5. []
  4. Belongia, E. A. & Naleway, A. L. (2003). Smallpox vaccine: the good, the bad, and the ugly. Clin Med Res, 1(2), 87-92.[]
  5. Aponte, J. J., Aide, P., Renom, M., Mandomando, I., Bassat, Q., Sacarlal, J. et al. (2007). Safety of the RTS,S/AS02D candidate malaria vaccine in infants living in a highly endemic area of Mozambique: a double blind randomised controlled phase I/IIb trial. Lancet, 370(9598), 1543-1551.[]
December 12th, 2007

Malaria eradication?

Eradicate Malaria India 1958 I’m marking final exams for the grad immunology class I teach, so I don’t have a lot of time to blog. But I do want to point to a really amazing, ambitious, and potentially world-changing initiative that doesn’t seem to have got the attention it deserves in the blog-world. A couple of months ago, Melinda Gates made a speech in which she said:

Bill and I believe that these advances in science and medicine, your promising research, and the rising concern of people around the world represent an historic opportunity not just to treat malaria or to control it-but to chart a long-term course to eradicate it.

I don’t need to give figures, I think, on what a devastating disease malaria is. The WHO fact sheet is filled with dismal stats (“A child dies of malaria every 30 seconds.“) And I’ve previously blogged about the track record of malaria vaccines, which have been encouraging but unsuccessful for forty years. Gates’ proposal really is (as she herself says) audacious, but I think she presents three excellent reasons for aiming for eradication:

  • the human cost of malaria
  • the financial cost. “If we plan only to control malaria, we will never eradicate it.
  • history, which tells us that any malaria control is just temporary: “the ability of the parasite to develop resistance to insecticides and medicines tells us that no set of control strategies can control malaria for very long.

Blogging on Peer-Reviewed ResearchProtect against malaria 1941 Is it possible? I have no idea, myself. It’s been tried before (the poster at the top is from 1958) without success, and we are certainly a long, long way away from that aim at the moment. I do think it’s a worthy goal. And there are some new glimmers of hope. A Lancet article1 that came out about the same time as Gates’ talk shows that a new malaria vaccine is safe and at least moderately effective.

Is “moderately effective” good enough? We don’t really know yet how effective the vaccine is; this study (which wasn’t designed to test effectiveness per se) found around a 65% level of protection — low for a vaccine in general; high for a malaria vaccine. A commentary on the paper in the same issue of Lancet2 says that “Some experts have predicted that the effect of the introduction of a partly protective vaccine will be reduction in morbidity and mortality in the first years of life, with negligible effect on transmission.” If so, then this is more a step toward control than eradication.

Still, it’s a step, and if in fact vaccination can reduce malaria at all then it’s a very promising step. Other vaccines are on their way, and the experience with this one will help in developing more and more effective approaches. As Epstein’s commentary3 says, “The next 5-10 years will probably be the most exciting in the long journey to bring a malaria vaccine to the developing world.


  1. APONTE, J., AIDE, P., RENOM, M., MANDOMANDO, I., BASSAT, Q., SACARLAL, J., MANACA, M., LAFUENTE, S., BARBOSA, A., LEACH, A. (2007). Safety of the RTS,S/AS02D candidate malaria vaccine in infants living in a highly endemic area of Mozambique: a double blind randomised controlled phase I/IIb trial. The Lancet, 370(9598), 1543-1551. DOI: 10.1016/S0140-6736(07)61542-6[]
  2. What will a partly protective malaria vaccine mean to mothers in Africa?Judith E Epstein The Lancet 370, 3 November 2007-9 November 2007, Pages 1523-1524 []
  3. What will a partly protective malaria vaccine mean to mothers in Africa? Judith E Epstein. The Lancet 370, 3 November 2007-9 November 2007, Pages 1523-1524 []
November 7th, 2007

Worms and allergies: A smoking gun?

Toxocara canis As everyone knows, the incidence of allergies and asthma has exploded over the past 50-odd years. As lots of people also know, while the reasons for this explosion isn’t known (and are probably complex) one of the popular concepts explaining this is the “hygiene hypothesis”. This was originally proposed way back in 1989:1

These observations . . . could be explained if allergic diseases were prevented by infection in early childhood, transmitted by unhygienic contact with older siblings, or acquired prenatally . . . Over the past century declining family size, improved household amenities and higher standards of personal cleanliness have reduced opportunities for cross-infection in young families. This may have resulted in more widespread clinical expression of atopic disease.

In the nearly 20 years since, this hypothesis hasn’t been proved or disproved. There are quite a few interesting correlations, and the underlying biology seems to make a lot of sense, but as least as far as I know there’s been no smoking-gun study that makes an undisputable link. A Nature Medicine paper2 from a couple of weeks ago adds a little more support to the hypothesis, and this one also holds out a distant hope of some kind of intervention as well. It’s long been known that parasitic worms — now rare in the West, but until recently a normal part of the human condition — induce an immune response that is broadly similar to a lot of allergic responses.

Blogging on Peer-Reviewed ResearchMelendez et al show that one class of parasitic worms make a protein that inhibits the anti-parasitic immune response. The protein, ES-62, does this by binding the pathogen pattern receptor molecule TLR4, thereby blocking a signalling pathway that ultimately leads to mast cell activation. This is presumably a parasite immune evasion molecule, analogous in concept to the many viral proteins that block TLR pathways. (The reason I say this is “presumably” a immune evasion molecule is that the other possibility is that the response is driven by the host — that this is more analogous to the way rodents develop a regulatory T cell response to persistent viruses, reducing harmful inflammatory diseases but allowing long-term infection with the virus.)

As the authors say, this is an exciting observation for two reasons. First, while not a smoking gun (that’s a rhetorical question in the title, OK?), it offers a mechanistic explanation for at least part of the hygience hypothesis. Second, the protein offers a handle for therapy of allergic diseases:

Suppression of mast-cell function by ES-62 offers a new explanation for the reason why people harboring worms of at least the filarial nematode type show reduced incidence of allergy, in spite of their elevated serum IgE. … By inhibiting mast-cell effector function, ES-62 offers a new potential therapeutic approach for diseases such as asthma, a medical problem of enormous importance in the developed world. Although ES-62 per se is unlikely to be used for treatment, enough is known about its structure and function to allow one to envisage the development of small, presumably phosphorylcholine-based, derivatives as drugs.


  1. Strachan, D. P. (1989). Hay fever, hygiene, and household size. BMJ 299, 1259-1260.[]
  2. Melendez, A. J., Harnett, M. M., Pushparaj, P. N., Wong, W. S. F., Tay, H. K., McSharry, C. P., and Harnett, W. (2007). Inhibition of Fc[epsi]RI-mediated mast cell responses by ES-62, a product of parasitic filarial nematodes. Nat Med 13, 1375-1381.[]
November 5th, 2007

Testing overdominance in MHC: Can it be done?

Plasmodium in mosquito midgut
Malaria parasites in mosquito midgut

Why is it so hard to come up with a disproof (or a proof) of overdominant selection in MHC?

I’m starting kind of in mid-sentence here, because this is a continuation of a series of posts on MHC diversity. Briefly: The major histocompatibility complex region in vertebrates is extraordinarily diverse — a hundred times more variable (more alleles) than the average genomic chunk. Even populations that are otherwise inbred and lack diversity throughout their genome, rapidly evolve, or maintain, MHC diversity. There is clearly powerful evolutionary selection for this diversity, and there are several different explanations as to what this driver might be. The two most plausible explanations are frequency-dependent selection (in which rare alleles are selected simply because they are rare, and pathogens haven’t adapted to them) and overdominance, or heterozygote advantage (where individuals with diverse MHC regions, containing many alleles, are selected because they are more resistant to pathogens).

Overdominance was (as far as I know) the first mechanism put forward to explain MHC diversity. 1 The concept is a simple one: If one MHC allele protects against disease by binding a certain set of peptides, then two alleles should protect against more diseases by cumulatively binding a larger set of peptides. A heterozygous individual should be more resistant to pathogens than individuals that are homozygous for either single allele.

This simple concept, though, turns out to be very difficult to test rigorously. Most importantly, several of the different predictions between overdominance and frequency-dependent selection depend on how the population evolves, over time; but when trying to test predictions, we are usually looking, more or less, at a static snapshot of evolution. In the static state, it’s much harder to differentiate between the two possibilities: Is the allele diversity we see a stable diversity (consistent with overdominance) or is it a dynamic diversity, with different alleles gaining and losing advantage as they become more or less frequent (consistent with frequency-dependent selection)?

True overdominance is explicitly not dependent on allele frequency. 2 There are conditions (that are not true overdominance) in which heterozygotes will have a selective advantage over homozygotes, where the advantage is strictly dependent on allele frequency. Therefore … 3

overrepresentation of HLA heterozygotes among individuals with favorable disease outcomes (which we term population heterozygote advantage) need not indicate allele-specific overdominance. On the contrary, partly due to a form of confounding by allele frequencies, population heterozygote advantage can occur under a very wide range of assumptions about the relationship between homozygote risk and heterozygote risk. In certain extreme cases, population heterozygote advantage can occur even when every heterozygote is at greater risk of being a case than either corresponding homozygote.

Blogging on Peer-Reviewed ResearchThere are a fair number of studies on more or less wild populations that have claimed to show evidence for overdominance, but few (if any) deal with the frequency problem. For that reason, most of the claims in the literature are at best consistent with overdominance, but are not proof of it.

A second complication is that individuals heterozygous at the MHC are quite likely to be heterozygous generally. How can specific effects of MHC heterozygosity be distinguished from a general heterozygote advantage? Again, this makes studies on wild populations hard to interpret cleanly.

There’s a third complication: Overdominance is most likely to be a factor in infections with more than one pathogen. 4

MHC-mediated resistance to a single pathogen is inherited as a dominant trait. This means that there will be no differences in susceptibility between a homozygote MHC allele or haplotype and a heterozygote carrying the focal allele plus a different one. Therefore, heterozygote advantage is difficult to detect in single pathogen challenges.

An exception to this might be when there’s technically a single pathogen, but it’s highly antigenically diverse — the obvious example being HIV, which mutates rapidly and regularly throws out antigenic variants during the course of infection. It’s interesting, then, that HIV infection is one of the situations where heterozygote advantage has been observed, 5 though I don’t think population allele frequency was taken into account in these studies. On the other hand, malaria is antigenically diverse as well, but experiments have not shown overdominance in that case.6

So we’re left with the difficult situation where you need to have fairly large numbers and multiple generations, in order to detect selection; yet you probably can’t use most natural populations to strictly the test the theory. Setting up a large and relatively diverse, yet well-controlled, lab animal population, and then infecting with multiple pathogens; or following a reasonably well-controlled field population; is a daunting task.

In the next post in this series I’ll mention a few cases where this has been done.


  1. Doherty, P. C., and Zinkernagel, R. M. (1975). A biological role for the major histocompatibility antigens. Lancet 1, 1406-1409.[]
  2. At least, that’s how I understand it; and I repeat that I’m not an expert. Anyone knowledgeable about this, feel free to jump in.[]
  3. Lipsitch, M., C. T. Bergstrom, and R. Antia. 2003. Effect of human leukocyte antigen heterozygosity on infectious disease outcome: the need for allele-specific measures. BMC Med Genet 4: 2. []
  4. Wegner, K. M., M. Kalbe, H. Schaschl, and T. B. Reusch. 2004. Parasites and individual major histocompatibility complex diversity–an optimal choice? Microbes Infect 6: 1110-1116. []
  5. For example, Carrington, M., G. W. Nelson, M. P. Martin, T. Kissner, D. Vlahov, J. J. Goedert, R. Kaslow, S. Buchbinder, K. Hoots, and S. J. O’Brien. 1999. HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science 283: 1748-1752. []
  6. Wedekind, C., Walker, M., and Little, T. J. (2005). The course of malaria in mice: major histocompatibility complex (MHC) effects, but no general MHC heterozygote advantage in single-strain infections. Genetics 170, 1427-1430.[]