Mystery Rays from Outer Space

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

November 30th, 2010

HIV evolution: individual vs. population

Worldwide HIV/AIDs Epidemic Statistics
Worldwide HIV/AIDs Epidemic Statistics

(We are in the process of selling one home and buying another, while at work I just finished organizing a course on biosecurity for an international group. In the upcoming week I’m traveling to a conference in Washington. To say nothing of the Thanksgiving holiday. All this means short and scarce updates for a little while.)

We know that the immune response to HIV forces the virus to evolve at great speeds, so that the viral targets of the immune response change and become at least temporarily invisible. We also know that the specific targets are different for almost every infected person. So although you have rapid evolution in each individual, what does this mean to overall evolution of the global population of HIV?

The several dozen CTL epitopes we survey from HIV-1 gag, RT and nef reveal a relatively sedate rate of evolution with average rates of escape measured in years and reversion in decades. For many epitopes in HIV, occasional rapid within-host evolution is not reflected in fast evolution at the population level.1

(My emphasis) This is a modeling study (though it did look at real-life data to some extent), but their conclusion is consistent with larger-scale population studies as well; see my previous post here and links therein.

  1. Fryer, H., Frater, J., Duda, A., Roberts, M., , ., Phillips, R., & McLean, A. (2010). Modelling the Evolution and Spread of HIV Immune Escape Mutants PLoS Pathogens, 6 (11) DOI: 10.1371/journal.ppat.1001196[]
October 7th, 2010

MHC vs pathogens: Evolution showdown

ShowdownI’m not finding time to give these papers a full post each, so let me pool together several in the same theme: MHC alleles and protection against pathogens.

It’s generally accepted that the reason there are so many MHC alleles is related to their ability to protect against pathogens.1 The version is probably the frequency-dependent selection model. According to this, pathogens are selected to be resistant to common MHC alleles, so individuals with rare alleles have a selective advantage and those alleles become more common, until pathogens are selected for resistance to them in turn. (Described in more detail here.).

The particular steps in this concept are each fairly straightforward and reasonably well supported. We know that different MHC alleles can be more or less effective against pathogens; we see some instances of pathogens developing resistance to particular MHC alleles, and so on. But it’s been quite difficult to put all the pieces together. The best examples of pathogens evolving resistance to MHC alleles, for instance, are within a single host, in the case of HIV. When we look at even this virus over a population instead, it’s much harder to detect any particular adaptation to MHC (though there may be some).

The problem is (probably) that we’re looking at a single frame of a movie. This is a dynamic process, as the pathogens and the individuals within a population co-evolve. It’s hard to see fossil MHC alleles and just as hard to see fossil viral epitopes. The snapshot we see today may be at any point along the process – the pathogen may have the upper hand, the hosts may, or they may be perfectly balanced. (Also, of course, the host need to deal with thousands of pathogens, while each pathogen may focus on one or a handful of hosts. It would take a fairly assertive pathogen to single-handedly push a host population toward differential allele usage. The host’s version of the movie frame would actually be a blur of a thousand frames from a thousand movies, each of which is shown at different speeds and with a different starting point, all overlapping and interacting with each other.)

So observations supporting the frequency-dependent model have been rather scarce; in fact, instances where MHC alleles differentially affect pathogens are themselves relatively scarce, and those are the starting points from which frequency-dependent selection arises. So I’m always intrigued when we learn of cases where there are specific resistance and susceptibility alleles of MHC for particular pathogens, in the wild, and in a population rather than an individual.

Here are some I’ve noticed in the past few weeks.

Koehler, R., Walsh, A., Saathoff, E., Tovanabutra, S., Arroyo, M., Currier, J., Maboko, L., Hoelsher, M., Robb, M., Michael, N., McCutchan, F., Kim, J., & Kijak, G. (2010). Class I HLA-A*7401 Is Associated with Protection from HIV-1 Acquisition and Disease Progression in Mbeya, Tanzania The Journal of Infectious Diseases DOI: 10.1086/656913

Other MHC class I alleles have been shown to be protective against HIV, so this is mainly adding to the list; but it;s a shortish list, so any additions are interesting.

MacNamara, A., Rowan, A., Hilburn, S., Kadolsky, U., Fujiwara, H., Suemori, K., Yasukawa, M., Taylor, G., Bangham, C., & Asquith, B. (2010). HLA Class I Binding of HBZ Determines Outcome in HTLV-1 Infection PLoS Pathogens, 6 (9) DOI: 10.1371/journal.ppat.1001117

An attempt to link observed protective MHC alleles, with the mechanism of protection, concluding that being able to induce T cell recognition of a specific HTLV-1 protein is associated with protection.  This is conceptually similar to the proposed mechanism by which [some] MHC alleles protect against HIV,2 where a specific peptide target can’t mutate away from T cell recognition.

Appanna, R., Ponnampalavanar, S., Lum Chai See, L., & Sekaran, S. (2010). Susceptible and Protective HLA Class 1 Alleles against Dengue Fever and Dengue Hemorrhagic Fever Patients in a Malaysian Population PLoS ONE, 5 (9) DOI: 10.1371/journal.pone.0013029

They identify MHC alleles that may be associated with protection against disease, and protection against severe disease.  I’m a little uncomfortable with the relatively small number of patients involved here (less than 100), and would like to see it confirmed in a larger study.

Guivier, E., Galan, M., Male, P., Kallio, E., Voutilainen, L., Henttonen, H., Olsson, G., Lundkvist, A., Tersago, K., Augot, D., Cosson, J., & Charbonnel, N. (2010). Associations between MHC genes and Puumala virus infection in Myodes glareolus are detected in wild populations, but not from experimental infection data Journal of General Virology, 91 (10), 2507-2512 DOI: 10.1099/vir.0.021600-0

We revealed significant genetic differentiation between PUUV-seronegative and -seropositive bank voles sampled in wild populations … Also, we found no significant associations between infection success and MHC alleles among laboratory-colonized bank voles, which is explained by a loss of genetic variability that occurred during the captivity of these voles.

The difference between wild and captive voles is reminiscent of the difficulty and confusion involved in MHC function in lab mice. In at least one set of experiments, it was necessary to have semi-feral mice before mechanisms could be teased apart.

  1. There are a few alternate explanations, but even things like the mate-selection hypothesis, which I discussed here and here, usually still involve an element of protection against pathogens.[]
  2. HIV and HTLV are related viruses, for what that’s worth[]
September 2nd, 2010

Immunity under natural selection

HapMap 3, officially announced in today’s issue of Nature,1 is an “integrated data set of common and rare alleles” in human populations, built from “1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations“. 

As well as being a resource for genome-wide studies, there are a number of things that can be done with the data directly. One of those is to help identify regions that are under positive natural selection. The authors found a number of them, including several immune-related genes in the Kenyan population.

A little sadly for me, none of these genes are ones I’m particularly familiar with. The three that are listed are:

  • CD226.  This is an activating NK cell receptor. An allelic variant in CD226 has been linked to a number of autoimmune diseases,2 so it wouldn’t be surprising to learn that it’s under some form of selection.  I didn’t check the actual SNP that was shown to be selected, to see if it’s the same one that’s linked to autoimmunity.

  • ITGAE.  This is an integrin3 that’s apparently involved in lymphocyte trafficking.  Allelic variants in ITGAE have been linked to a number of diseases including sarcoidosis4 and ischemic stroke.5

  • DPP7 is dipeptidyl-peptidase 7.  Although I’ve had a strong interest in peptidases for a while6 because of their influence on MHC class I antigen presentation, DPP7 seems to have an unrelated role, that of preventing apoptosis of resting lymphocytes. I don’t know of any links between DPP7 and disease, but obviously altering lymphocyte survival could impact lots of things. 

I’m sure that any more immune-related genes are under strong selection — we know that MHC genes are very strongly and rapidly selected, for example — but they don’t necessarily send up flags in this sort of analysis. 

  1. The International HapMap 3 Consortium (2010). Integrating common and rare genetic variation in diverse human populations Nature, 47, 52-58 DOI: 10.1038/nature09298[]
  2. Douroudis K, Kingo K, Silm H, Reimann E, Traks T, Vasar E, & Kõks S (2010). The CD226 Gly307Ser gene polymorphism is associated with severity of psoriasis. Journal of dermatological science, 58 (2), 160-1 PMID: 20399620

    Maiti AK, Kim-Howard X, Viswanathan P, Guillén L, Qian X, Rojas-Villarraga A, Sun C, Cañas C, Tobón GJ, Matsuda K, Shen N, Cherñavsky AC, Anaya JM, & Nath SK (2010). Non-synonymous variant (Gly307Ser) in CD226 is associated with susceptibility to multiple autoimmune diseases. Rheumatology (Oxford, England), 49 (7), 1239-44 PMID: 20338887[]

  3. Intergrins are cell-surface molecules often involved in cell-cell interactions[]
  4. Heron M, Grutters JC, Van Moorsel CH, Ruven HJ, Kazemier KM, Claessen AM, & Van den Bosch JM (2009). Effect of variation in ITGAE on risk of sarcoidosis, CD103 expression, and chest radiography. Clinical immunology (Orlando, Fla.), 133 (1), 117-25 PMID: 19604725[]
  5. Luke MM, O’Meara ES, Rowland CM, Shiffman D, Bare LA, Arellano AR, Longstreth WT Jr, Lumley T, Rice K, Tracy RP, Devlin JJ, & Psaty BM (2009). Gene variants associated with ischemic stroke: the cardiovascular health study. Stroke; a journal of cerebral circulation, 40 (2), 363-8 PMID: 19023099[]
  6. Pubmed link to my peptidase papers[]
August 19th, 2010

And so on, ad infinitum

Rosy Apple Aphid (Whalon lab)
Rosy Apple Aphid (Whalon lab, MSU)

Normally I don’t talk about research that’s well covered elsewhere, but I like this one so much (and it links back to so many of my earlier posts; check the footnotes for those links) that I’ll make an exception here.  I’d seen bits and pieces of this story, but I didn’t have the big picture until I listened to Carl Zimmer’s1 latest Meet The Scientist podcast2 where he interviewed Nancy Moran.3

So this is kind of about insect immunity. Insects have lots of innate immune responses, the short-term sorts of things that in vertebrates we call ‘inflammation’, but they don’t have the long-term adaptive responses 4 that incorporate antibodies and T cells — those systems arose in sharks and their progeny (and, apparently mostly independently, in lampreys and hagfish,5 but that’s a different story).

The hallmark of adaptive immunity, in contrast to innate immunity, is its flexibility: Different responses for different agents, and capable of changing as the target changes.  So insects can’t do that, although of course their immune system has worked pretty well for a few hundred million years.

Except aphids have a sort of changable immune response.  How does that work?

Parasitic wasp of aphids
Parasitic wasp laying eggs in an aphid
University of Wisconsin)

This is an immune response, not to bacteria or viruses, but to parasitic wasps.  Aphids are popular targets for some of these wasps: The wasps lay eggs in the aphid, the eggs hatch into baby wasps, and the baby wasps eat the aphids from the inside out until they kill the aphid and then they fly away to predate some more.  Except in some aphids, the baby wasps are killed as they hatch, and the aphids survives to make more aphids.

And this immunity to the wasps is — on a population basis, not an individual basis — rather flexible. Insects in general are good at evolving toxin resistance over years or decades, but aphids have apparently been doing this over millions of years. It turns out that different aphids kill the baby wasps in different ways, using different toxins to do so, and the toxins change over time as well.  So the wasps can’t develop resistance to the toxins.  It’s a little bit — a very little bit — like an adaptive immune system, at least in broad terms.

Not all aphids are immune at all (or there would be no wasps).  You can take susceptible aphids and make them resistant, though. You just have to infect them with a particular bacterium.  This is a symbiotic6 bacterium, that only lives in aphids — it’s dependent on the aphid host to provide it with essential nutrients — and these bacteria carry toxin genes. They help their host survive by providing toxin genes, that kill the wasps that parasitize the hosts the bacteria are symbiotic with.

But not so fast! The bacteria don’t naturally have toxins! The toxins come from parasites of the bacteria! There are bacteriophages, viruses that infect the bacteria, that carry the toxins.  When the viruses parasitize the bacteria that are parasitizing the aphids, then the parasitic wasps can’t parasitize the aphids that are hosting the bacteria that are hosting the viruses!

And if you look at the bacteriophages as a population, they have a section of their genome that is highly diverse. That part is the region that carries the toxin. Different phages, different toxins, that can spread to new bacteria and then to new aphids, so the aphids can have a supply of new toxins to take care of newly-resistant wasps.

Just to make this even more complex, you know how the wasps subdue their prey? They inject in a complex mix of toxins that shut down the insect immune system. Guess where those toxins come from?7 From the symbiotic viruses8  that the wasps have incorporated into their own genomes millions of years ago, that carry immune evasion genes that the wasps have adapted to use to subdue the aphids that carry the bacteria that carry the viruses that provide the toxins that protect the aphids against the wasps that carry their own viruses to attack the aphids.

  1. Ed Yong also covered this story last year.[]
  2. By the way, you all should be listening to Meet the Scientist.  Zimmer is not only an excellent writer, he does a really good interview, and the scientists he interviews are all highly articulate and interesting.  Scientists as a group tend to be pretty articulate about their work, because communication is actually part of the job description, but Zimmer is very good about asking the right questions and then getting out of the way.[]
  3. A few of the papers by Moran and her colleagues:
    • Oliver KM, Degnan PH, Hunter MS, & Moran NA (2009). Bacteriophages encode factors required for protection in a symbiotic mutualism. Science (New York, N.Y.), 325 (5943), 992-4 PMID: 19696350
    • Degnan PH, Yu Y, Sisneros N, Wing RA, & Moran NA (2009). Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proceedings of the National Academy of Sciences of the United States of America, 106 (22), 9063-8 PMID: 19451630
    • Degnan PH, & Moran NA (2008). Evolutionary genetics of a defensive facultative symbiont of insects: exchange of toxin-encoding bacteriophage. Molecular ecology, 17 (3), 916-29 PMID: 18179430
    • Degnan PH, & Moran NA (2008). Diverse phage-encoded toxins in a protective insect endosymbiont. Applied and environmental microbiology, 74 (21), 6782-91 PMID: 18791000[]
  4. Earlier posts on insect immunity:
    Invertebrate memory, or wishful thinking?
    “Social immunity” in ants?
    “Social immunity” followup []
  5. Posts on lamprey and hagfish immunity:
    Same trip, different routes: Lamprey immunity
    Lampreys got antibodies
    Lamprey VLR and antigen binding
    Lamprey immunity, again[]
  6. Posts on other arthropods and their symbiotic viruses and bacteria:
    How the aphid got its wings
    More symbionts and flight []
  7. To be honest, I didn’t check the kinds of wasp here, so I don’t know for sure that these are among the families of wasps that do this[]
  8. Posts on wasps and their symbiotic viruses:
    Bioweaponized wasps
    Not merely bioweaponized, but mutualistic bioweaponized wasps[]
August 17th, 2010

Pigs (and their viruses) fly

Type II PRRSV An emerging disease that I just missed directly seeing emerge is PRRS.

PRRS is “porcine reproductive and respiratory syndrome”, which pretty much sums up the disease. It’s caused by — you’ll never guess — Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus that emerged in 1987. That was the year I left large animal veterinary practice, so I never had a chance to deal with PRRS clinically.

Twenty-three years may not seem like all that long a time, but if you’re an RNA virus that’s a lot of generation times and a whole lot of time for mutations and evolution, and PRRS viruses are an evolutionarily mess. 1 There are North American type PRRSV viruses and European type viruses, there are mysterious clusters of related viruses, there are clusters of related diseases, there are thousands of sequences, and it’s just kind of baffling what’s gone on with the whole schtick.

A new paper2 has tried to sort out part of the mess by analyzing some 8624 North American-type PRRSV sequences, from nearly a dozen countries, and working out evolutionary relationships between them all. 3 (The focus on the North American series — the Type II PRRSV — is because this group seems to be a more common source of disease; although the European strains are far from rare themselves.)

There were a couple of interesting points that parallel some other viruses:

1. Feral vaccines. It’s already known, or at least strongly suspected, that some of the modified-live PRRSV vaccines have started to go feral on a small scale (not nearly as dramatically as the vaccinia virus I mentioned a while ago), and that’s supported by this genetic analysis:

In the vaccine-associated sublineage phylogenies (data not shown), there were a number of well-supported small clusters that might reflect the small-scale transmission of the vaccine viruses in the field … 2

As well as vaccinia, there are other live vaccines that are known to spread into the population. The sort of limited transmission that seems to be showing up here is more typical of this sort of thing than are the vaccinia instances I talked about before.

2. The amazing flying pigs. Even though this is just one of the two major sub-groups of PRRSV and it’s less than 25 years since it emerged, they came up with nine fairly distinct lineages of the virus (see the figure to the right). As you’d expect the lineages speak to the history of the virus — which is to a large extent the history of the pigs that carried the virus.4

This version of the virus probably started out in North America (though how it got there … ?) and then got introduced into other countries on several independent occasions. Two of these introductions were in the late 1980s, shortly after the North American emergence. Aside from that there’s evidence of a bunch of smaller introductions:

… lineage 1 had several Thai sequences clustered with early Canadian sequences … ; lineage 8 contained highly pathogenic Chinese strains and their relatives … ; and lineages 8 and 9 had several Italian isolates which were distributed separately along the phylogeny …, indicating independent introductions of PRRSV from the United States to Italy. 2

They were even able to identify smaller-scale travel patterns, between individual states in the USA:

Iowa plays a central role because its viruses were introduced recurrently to all nine other states (Fig. 5B). The remaining states were not just receiving sites. Their local strains also were transmitted to other states repeatedly, but within a narrower range. … Our phylogeographic analyses reveal, for the first time, an interstate PRRSV traffic network in the United States. … The result also indicates that long-distance spread is a frequent process for PRRSV … 2

This is a reminiscent of the history of the pandemic H1N1 influenza virus, when it was still in swine. (Remember that pandemic H1N1 is genetically  a mixture of a North American swine influenza strain and a Eurasian strain.)  There’s a large national and global traffic in pigs, and even though most countries are reasonably careful in the way they handle incoming pigs it’s not a guarantee against virus introduction. I’m not singling out pigs, either — other kinds of livestock also are global travellers, and obviously so are humans.  But it’s a reminder that it isn’t just humans and their viruses that can quickly travel and spread around the globe.

  1. More correctly, our understanding of their evolution is a mess. The viruses are doing just fine.[]
  2. Shi, M., Lam, T., Hon, C., Murtaugh, M., Davies, P., Hui, R., Li, J., Wong, L., Yip, C., Jiang, J., & Leung, F. (2010). Phylogeny-Based Evolutionary, Demographical, and Geographical Dissection of North American Type 2 Porcine Reproductive and Respiratory Syndrome Viruses Journal of Virology, 84 (17), 8700-8711 DOI: 10.1128/JVI.02551-09[][][][]
  3. That’s a lot of viruses, but the sampling is heavily biased to a limited number of places, especially the USA [and especially a few regions within the USA] so it’s probably an underestimate, and maybe a severe underestimate, of the global diversity.

    I didn’t know, by the way, that there’s a PRRSV Database:[]

  4. Or of the pig’s fluids. I think that especially in the early days of the emergence, the virus was spread by the boar semen used for artificial insemination.[]
August 10th, 2010

DNA virus quasispecies? (Probably not.)

I’ve talked about quasispecies several times, and emphasized that RNA viruses, with their high replication error rates, are most prone to forming quasispecies.

I’ve also pointed out, though, that actually measuring quasispecies is technically difficult, and measuring it for the larger DNA viruses would be even harder. You’d need to run sequences on many viral genomes, to see how much variation develops over time; and it’s only recently that sequencing tech has approached the point where it’s even thinkable, let alone affordable, to do that:

While large DNA viruses are thought to have low mutation rates, only a small fraction of their genomes have been analyzed at the single-nucleotide level.1

So maybe DNA viruses might actually form quasispecies, and we don’t know it?

In fact, even for DNA viruses, mutants appear fairly quickly, given the appropriate selection pressure. In principle, these might not even be new mutations, but simply expansion of a particular part of a quasispecies that was already pre-existing. (It’s probably a fairly obvious point, but it’s important to remember that the introduction of new mutants, and their selection and expansion, are completely different processes. Some viruses throw out incredible numbers of mutants, but almost all of them are dead ends that are actively selected against, or at the least not selected for. Other viruses may make far fewer mutants, but given strong enough selection pressure some of these might rapidly take over the population. It’s very tricky to use observed mutations as a measure of mutation frequency, because observation often depends on selection to build up the numbers of the mutant before you can see it.)

At any rate, it’s a fair enough question,2 but recently there has been some evidence that supports the concept of DNA virus genome stability. Wayne Yokoyama’s lab has actually sequenced multiple genomes of mouse cytomegalovirus (a large DNA virus — a member of the herpesvirus family) to look at quasispecies.1

One of the things they did find was a significant number of variations in their stock, compared to the stock they had got it from years before:

… our laboratory’s Smith strain MCMV differed from the previously published Smith strain … There were 452 differences, including 50 insertion/deletions (indels) and 402 single-bp substitutions. … this high number of differences suggested that MCMV mutated in vivo, as we had previously maintained our MCMV stock by in vivo passages. 1

In other words, the standard methods of maintaining a virus — repeatedly growing new stocks in cells, and using those new stocks to make yet more — allow the accumulation of variations in the genome — which is already well known, of course, but often neglected in lab experiments.  Again, as I point out above, the number of observed mutations we see here doesn’t tell us much about the actual mutation frequency.

How often do mutations arise? By running the virus through cells repeatedly (in vitro, that is) and then seeing how individual clones differed, they determined that there are very, very few mutations per replication. What’s more, and even more impressively, very few mutations appeared after passages through mice (in vivo):

… the remaining 9 mutations allowed us to estimate the mutation rate of MCMV as 1.0 x 10–7 mutations per bp per day after in vivo passage, very similar to the mutation rate calculated for in vitro passage.1

(My emphasis) For comparison, the MCMV genome is not quite 250,000 bp long, so we’re looking at around one mutation per 40-50 genomes per day (if I’m dividing right). That’s hundreds of times more stable than most RNA viruses (see the table here3 for some RNA virus error rates).  Still, there’s plenty of room for natural selection in there, because of course there are hundreds or thousands of new MCMV genomes being made per day even in the most conservative estimate (and maybe more like millions or hundreds of millions), so dozens to thousands of them are mutants.

So, not surprisingly, Yokoyama’s group was able to detect a cluster of mutations that were almost certainly selected in the mouse; without going into detail, these mutations were in a viral gene (m157) that’s known to be recognized by the (laboratory) mouse immune system, so it wasn’t surprising that mutants were selected. And such mutants did not appear in mice without the appropriate immune component, demonstrating the role of natural selection in this cluster.

They offer a number of cautions, including one that’s raised in almost all such studies:

One caveat to our mutation analysis is that lethal mutations were probably underrepresented in the final DNA pool since, by definition, they did not propagate. Nonetheless, this limitation is intrinsic to all mutation analysis.1

Still, the results are solid and reassuring, supporting a basic concept in viral evolution.

  1. Cheng, T., Valentine, M., Gao, J., Pingel, J., & Yokoyama, W. (2009). Stability of Murine Cytomegalovirus Genome after In Vitro and In Vivo Passage Journal of Virology, 84 (5), 2623-2628 DOI: 10.1128/JVI.02142-09[][][][][]
  2. Well asked, invisible non-existent person![]
  3. CASTRO, C., ARNOLD, J., & CAMERON, C. (2005). Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective. Virus Research, 107 (2), 141-149 DOI:10.1016/j.virusres.2004.11.004[]
August 3rd, 2010

Lamprey immunity, again

The Lamprey (Yarrell 1835)
From A History of British Fish (William Yarrell, 1835)

I’ve talked about lamprey immune systems several times (here, here, and here). I find them fascinating because it shows both how our own immune system developed, and also shows alternate routes that can lead to a pretty good, but very different, immune system.

Quick background: In order of evolutionary appearance you have sea urchins, lampreys, sharks, reptiles, mammals. (Note that this is not true, it’s no more than a sloppy shorthand for common ancestry, but it’s a handy shorthand for this purpose.  See a phylogenetic tree here.) Mammals have a form of adaptive immune system that includes T lymphocytes and antibodies, and at first glance this whole complex system arose, almost fully-formed, in sharks.1

This has always amazed me, because an adaptive immune system doesn’t work in isolation; the pieces don’t work alone. You need all kinds of moving parts — all the complex molecular pieces that chop and snip DNA to form T cell receptors and antibodies, all the multiple parts of a thymus that screen T cells for functional and safe receptors, the MHC molecules that the receptors see and all the pieces that snip and shuffle around peptides for that system, the spleen and lymph nodes that let lymphocytes interact with other cells, — and it seemed that all these pieces abruptly appeared and put themselves together, like a fine watch, in one evolutionary blink.

When I first learned about this, some 15 or 20 years ago, I told myself that this was an illusion, that once more species were looked at we’d see the history of these moving parts in other common ancestors. Of course, this is exactly what’s happened since then. We see accidental, random parts in sea urchin genomes (I talk about that here) and we see other bits and pieces arising in lampreys and hagfish (in the links at the top).

So in reality, the adaptive immune system didn’t arise all that suddenly after all; the pieces gradually were added over a hundred million years or more, sometimes purely by chance, sometimes for other purposes altogether, and sometimes as components of a prototypic immune system that acted as a foundation for the whole shark thing.2

So that’s the first part of the background: In lampreys, which diverged from the mammalian lineage maybe 450 million years ago, we see many of the pieces of a mammalian adaptive immune system. There are cells that look a lot like lymphocytes, there is something that looks like a spleen. But, as I say, there are none of the familiar pieces that we think of as an adaptive immune system. Lampreys flatly do not have our adaptive immune system:

Nevertheless, the cardinal elements of adaptive immunity, namely Ig, TCR, RAG1 and 2, and MHC class I and II, were conspicuously absent.3

Lamprey "antibody"
Lamprey variable receptor with bound antigen4

But step back a little, and look a little deeper, and we see some familiar parts. Lampreys do, in fact, have variable receptors, just like T cell receptors and antibodies, and those receptors are made by chopping and shuffling genome DNA, just like TcR and antibodies, and are expressed in their lymphocyte-like cells, and some are secreted (like antibodies and B cells) and some are cell-associated (like T cell receptors).

And here’s the other amazing thing: At the molecular level, the lamprey receptors are completely unlike T and B cell receptors. The lamprey lineage came up with a completely different system that allows them to do pretty much the same thing as the shark lineage. Their receptors are different kinds of molecules, and the system that shuffles the genomic DNA is different. 5 Yet, the functional end product is the same — a system that has immunological memory. An adaptive immune response, that’s quite alien to our own, but that works pretty damn well.

Although the Ig-based and VLR-based adaptive immune systems in jawed and jawless vertebrates use different genes and assembly mechanisms, both systems generate diverse repertoires of anticipatory receptors capable of recognizing almost any Ag through the combinatorial assembly of large arrays of partial gene segments. The development of clonally diverse lymphocytes allows for Ag-specific responses and memory, which are lacking in innate immunity.3

There is still a lot we don’t know about lamprey immunity (how does it present self-reative receptors, with no thymus?) but what we do know is just so amazing, I’m completely fascinated by it. It beautifully illustrates two of the basic features of evolution — building on previous structures, whether related or not; and alternate solutions to the same problem. Herrrin and Cooper have a short and dense, but very interesting, review, 3 that prompted this particular post.

  1. That is, in the common ancestor of sharks and mammals, to use a slightly less-sloppy terminology.[]
  2. And of course, the system has continued to evolve. The mammalian system is remarkably similar to the shark in broad strokes, but it’s also very different in many ways.[]
  3. Herrin, B., & Cooper, M. (2010). Alternative Adaptive Immunity in Jawless Vertebrates The Journal of Immunology, 185 (3), 1367-1374 DOI: 10.4049/jimmunol.0903128[][][]
  4. B. W. Han, B. R. Herrin, M. D. Cooper, I. A. Wilson (2008). Antigen Recognition by Variable Lymphocyte ReceptorsScience, 321 (5897), 1834-1837 DOI: 10.1126/science.1162484[]
  5. Though there are some common pieces that hint at a common ancestor of the two systems, maybe.[]
July 29th, 2010

Genetic ironies: Retrovirus version

I’ve mentioned the APOBEC family before (for example, here and here). They’re a group of mammalian genes that (among other things) protect against retrovirus infection.

DIfferent strains of mice have different resistance to retrovirus infection. Some strains are highly resistant, others quite susceptible. At least some of this difference in susceptibility comes down to different expression levels of mouse APOBEC3: High expression of the gene gives good resistance to some retroviruses, low expression gives less resistance.

How come some strains have higher expression than others? Turns out that it’s because a retrovirus inserted in the APOBEC3 region of the genome of certain mouse strains, and that insertion cranks up expression of the APOBEC3.

We discovered that the mA3 allele in virus resistant mice is disrupted by insertion of the regulatory sequences of a mouse leukemia virus, and this insertion is associated with enhanced mA3 expression.  ((Sanville, B., Dolan, M., Wollenberg, K., Yan, Y., Martin, C., Yeung, M., Strebel, K., Buckler-White, A., & Kozak, C. (2010). Adaptive Evolution of Mus Apobec3 Includes Retroviral Insertion and Positive Selection at Two Clusters of Residues Flanking the Substrate Groove PLoS Pathogens, 6 (7) DOI: 10.1371/journal.ppat.1000974))

So perhaps low APOBEC expression allowed retrovirus infection, which led to insertion of the retrovirus genome, which increased APOBEC3 expression and provided resistance to further retrovirus infection.

July 26th, 2010

Quasispecies thoughts

Quasispecies theory predicts that slower replicators will be favored if they give rise to progeny that are on average more fit; these populations occupy short, flat regions of the fitness landscape … Flat quasispecies accept mutation without a corresponding effect on fitness … A flat quasispecies with an expansive mutant repertoire can explore vast regions of sequence space without consequence and is poised to adapt to rapid environmental change.

Lauring, A., & Andino, R. (2010). Quasispecies Theory and the Behavior of RNA Viruses PLoS Pathogens, 6 (7) DOI: 10.1371/journal.ppat.1001005

(My emphasis)  RNA viruses in general form quasispecies because they have such high mutation rates.  Many (though by no means all) emerging infections are the result of RNA viruses. I’ve pointed before to aspects of viruses that might help them jump from species to species (for example, here — though this is a DNA virus, not an RNA virus, and I don’t think it runs in quasispecies — and the string of posts I link to inside that one).

One example Lauring and Andino point to is influenza virus hemagglutinin (HA). Influenza mutates very rapidly, of course, but most of the changes are harmful to the virus. But changes in HA seem to be very well tolerated. Since HA is a major target of the immune system, this property allows influenza to avoid the immune system without getting hit by defects in fitness associated with the immune evasion.  This is a contrast to, say, HIV (generalizing here! This isn’t always true). HIV within a patient undergoes constant changes to avoid the immune response, but many of these changes reduce the overall viral fitness. If you take the mutated HIV into an environment without that particular immune response, the virus quickly mutates back to its original, more-fit, form.

I’m not sure how we would assess, in advance, which viruses are more “flat” than others and that are therefore more able to adapt to new species, but it’s something to think about as we look at new viruses and new viral variants. I would be interested in SARS, for example — what happened to mutation tolerance as the virus adapted to humans? Was the virus that originally jumped into humans different in this was from the ones that normally infect bats? Not easy to measure, though.

July 12th, 2010

Short takes: Deep sequencing and HIV drug resistance

Short comments about what I’ve been reading (besides several hundred influenza articles):

Hedskog, C., Mild, M., Jernberg, J., Sherwood, E., Bratt, G., Leitner, T., Lundeberg, J., Andersson, B., & Albert, J. (2010). Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing PLoS ONE, 5 (7) DOI: 10.1371/journal.pone.0011345

The whole deep sequencing thing is going to profoundly change our knowledge of viral pathogenesis, as well as their ecology.

With highly mutation-prone viruses like HIV, hepatitis C virus, or influenza, our understanding of genome sequences has been based on the overall average genome — the average of a vast and diverse population. That average, that we’ve been calling the genome of these viruses, may not even exist as such, and certainly the minor variants that have been missed by traditional methods are also critically important, because they can explode out within a few days to take over the entire population, given the right set of circumstances. For example, if among those minor variants there are a few drug-resistant strains, then as soon as you treat the host, those variants may be able to take over.

In this paper, deep sequencing of people with HIV shows that drug-resistant variants do exist even before treatment, but they are normally very rare. They can take over during treatment with the particular drug, but when treatment is stopped they rapidly regress to rarity. This is presumably because the drug resistance makes the virus globally less fit (in the natural selection meaning of the term). When their more-fit brethren are destroyed by a drug these crippled, but drug-resistant, variants can grow out, but remove that selective pressure and the more wild-type versions take over once again.

As well as implications for treatment, this tells us something about viral reserves:

In most patients, drug resistant variants were replaced by wild-type variants identical to those present before treatment, suggesting rebound from latent reservoirs. 1

  1. Hedskog, C., Mild, M., Jernberg, J., Sherwood, E., Bratt, G., Leitner, T., Lundeberg, J., Andersson, B., & Albert, J. (2010). Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing PLoS ONE, 5 (7) DOI: 10.1371/journal.pone.0011345[]