Mystery Rays from Outer Space

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

June 5th, 2008

On HIV vaccines

Particularly important are questions regarding the effect of the quality, quantity and specificity of the vaccine-induced CD8 T-cell response on post-infection viral load control. These questions could not be addressed without a vaccine approach that actually induced CD8 T-cell responses in most recipients.

The Merck vaccine was the first such candidate, so it is a misleading exaggeration to claim that its failure is a “crisis” for HIV vaccine research. A journal with Nature’s long history is well placed to know how likely first-time successes are in science.

–Richard Jefferys,1 in Correspondence to Nature:
Vaccine failure is not a ‘crisis’ for HIV research
Nature 453, 719-720 (5 June 2008) | doi:10.1038/453719d


  1. See the Michael Palm Basic Science, Vaccines & Prevention Project Weblog[]
June 4th, 2008

Hypermutation as a weapon

Mutation comicHIV mutates at extraordinary speed, allowing it to throw out mutants that are at least temporarily invisible to cytotoxic T lymphocytes. We also know, of course, that anti-retroviral drugs (if used alone) are often only temporarily effective against HIV, until the virus mutates and develops resistance to the drug. On the other hand, there are apparently some HIV infections, long-term non-progressors, in which the virus isn’t able to find an effective immune escape strategy; the roads to evasion in these people travel over too many mountains for the virus to scale. When looking at potential new anti-HIV therapy, one of the questions has to be how quickly the virus can discover a path to drug resistance.

One of the relatively recent exciting findings in retrovirology1 is the APOBEC gene family’s role in blocking viral infection. The APOBECs are a largish family of enzymes, of which a few seem to exist mainly to prevent retrovirus replication. In humans, APOBEC3G (as well as some other APOBEC family members) seems to be a fairly important anti-retroviral protein; but it doesn’t help against HIV much, because HIV has evolved an immune evasion gene that blocks APOBEC3G’s effect. (A nice review is at my colleague Yong-Hui’s site.)

This is the vif (“viral infectivity”) protein. vif prevents APOBEC3G from damaging the viral genome by forcing it (APOBEC3G) to be destroyed by the proteasome;2 this is yet another instance of the immune evasion arms race between host and virus, in which each side alternately develops new weapons and defenses. (It’s also a reason for host restriction, since HIV vif doesn’t work against APOBECs from many non-human species.)

APOBEC3GWithout vif, newly formed HIV virions end up incorporating APOBEC into their capsids as they form. APOBEC forces hypermutation of the HIV genome, which is enough to destroy the virus (some mutation is good, but massive hypermutation is bad).

Mutant HIV that don’t have vif are profoundly defective in cells that contain APOBEC3G,3 That makes the vif/APOBEC interaction an attactive drug target.4 If you can prevent vif from destroying APOBECs, then you allow APOBECs to do their jobs and prevent HIV from replicating and spreading.

But will it work? Or is this just another bump in the road for HIV, a little hill that the virus can mutate around by developing resistance to APOBEC even without vif?

APOBEC + vif (Kao et al 2004)The answer5 seems to be that it has a reasonable chance of working, though there’s no guarantee.

The experiment was to grow vif-negative HIV in a cell line that has APOBEC3G and see how often resistant viruses grew out; also, how long it took to see the resistant set, and what mutations enabled the virus to resist APOBEC3G activity.

Just three resistant viruses, out of 48 attempts, grew out by about five weeks of culture. That’s a reasonably good success rate, especially as all three of the mutants turned out to still be susceptible to other APOBECs. That is, although vif confers resistance to APOBEC3G and 3F, these mutants were resistant only to 3G. An anti-vif therapeutic would presumably be even more effective, because 3F would still be active. 6

Our studies therefore provide strong additional justifications for efforts to develop Vif-neutralizing therapeutics.

The interesting thing was how these mutants had evolved resistance. Rather than reactivating vif or some parallel pathway, they had apparently discovered an altogether new way of reducing APOBEC3G damage.

It took a double mutation to escape. One of the mutatations seems to be simply making more virus. APOBEC3G acts when it’s packaged in viral particles; more viral particles means the APOBEC3G is diluted more, so there’s less per virus.

The other mutation truncated another viral gene, vpr, raising the possibility that vpr actually increases HIV susceptibility to APOBEC3G:

These unexpected results suggested that Vpr might actually facilitate APOBEC3G-dependent restriction by, for instance, packaging a cellular factor.

Finally, the authors raise the possibility that the mutant HIV might have discovered a solution already in use by other viruses:

the APOBEC3G “resistance by tolerance” mechanism described here might well apply to many viruses. … Therefore, the ability to tolerate and perhaps even regulate APOBEC3-dependent restriction has clear implications for virus evolution, immune escape, and drug resistance.


  1. Sheehy AM, Gaddis NC, Choi JD, Malim MH (2002) Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature 418:646-650.[]
  2. Sheehy AM, Gaddis NC, Malim MH (2003) The antiretroviral enzyme APOBEC3G is degraded by the proteasome in response to HIV-1 Vif. Nat Med 9:1404-1407.[]
  3. Lecossier D, Bouchonnet F, Clavel F, Hance AJ (2003) Hypermutation of HIV-1 DNA in the absence of the Vif protein. Science 300:1112.[]
  4. For example: Izumi T, Shirakawa K, Takaori-Kondo A (2008) Cytidine deaminases as a weapon against retroviruses and a new target for antiviral therapy. Mini Rev Med Chem 8:231-238.[]
  5. Hache G, Shindo K, Albin JS, Harris RS (2008) Evolution of HIV-1 Isolates that Use a Novel Vif-Independent Mechanism to Resist Restriction by Human APOBEC3G. Curr Biol 18:819-824 []
  6. On the other hand, a therapeutic might be easier to escape from by mutating vif away from, say, the drug binding site. This experiment wasn’t designed to test that, but rather the underlying question of whether attacking vif is a good long-term strategy in the first place.[]
June 2nd, 2008

On chemotherapy and tumor immunity

… it may be important to readdress the therapeutic management of different cancers, given the idea that chemotherapy should elicit an immune response.  …  it could be important to preserve the sentinel lymph node rather than remove it systematically for disease staging purposes. Indeed, the sentinel lymph node constitutes the privileged site of antigen priming, in which the presence of activated DCs (expressing DC-LAMP – a protein only expressed in mature DCs) constitutes a positive prognostic marker, at least in melanoma.

The anticancer immune response: indispensable for therapeutic success?
Laurence Zitvogel, Lionel Apetoh, Francois Ghiringhelli, Fabrice Andre, Antoine Tesniere and Guido Kroemer. J. Clin. Invest. 118(6): 1991-2001 (2008). doi:10.1172/JCI35180.

June 1st, 2008

Viral speciation and host restriction

phi-6 bacteriophageThe viruses I’m particularly interested in, herpesviruses and adenoviruses, tend to have a limited host range. For example, human cytomegalovirus doesn’t infect mice, and mouse cytomegalovirus doesn’t infect humans. Some of the reasons underlying these host specificities are starting to be mapped out at the molecular level (I’ve talked about a couple of examples here). A larger question, though, is why viruses become host-restricted in the first place. After all, a few viruses, such as rabies, are able to infect a huge range of species. Presumably it would benefit a virus to have a wider range of potential hosts available. Why haven’t more viruses evolved ways of infecting many species?

Part of the answer is presumably that it’s a hard enough task for a virus to infect a single host, and the more fine-tuned to one host a virus becomes, the less well-adapted to other hosts it is. We see this, perhaps, in influenza viruses; those that are adapted well to infecting birds are poorly adapted to infecting humans, at least partially because their receptors are better suited to binding molecules. (But let’s not lose track of the fact that avian influenza viruses are nevertheless capable of infecting many species of birds, making them much more versatile than cytomegaloviruses and their ilk.) But this is kind of a hand-waving answer, based on hunches and guesswork. I’d like to see a more formal test of the hypothesis.

A paper published in Evolution last fall1 takes a run at explaining host restriction. It’s far enough from my fields that I don’t want to critique it in great detail, but it makes some intriguing suggestions, some of which ring truer than others to me.

Apple maggot flyDuffy et al. argue that speciation and host adaptation are tightly linked. (That was what caught my attention, because for the most part you get a new herpesvirus when its host speciates; so you have a combination of reproductive isolation and tight host adaptation.) Speciation, at least in this context, means reproductive isolation. The way viruses become reproductively isolated is when they can’t infect the same host; so for viruses “reproductive isolation” is the same as “host restriction”. Duffy et al here are using host restriction as a model for ecological adaptation; one of the analogies they use is the famous apple maggot fly, which has developed reproductive isolation by breeding on fruit with different ripening times.

There’s some previous work on this in viruses; I wasn’t familiar with it, though, and the reviews2 are not easily accessible to me right now:

Previous experiments have shown that viral adaptation to a single host is often accompanied by a reduced ability to infect alternative hosts … For example, adaptation of the bacteriophage X174 to Salmonella enterica was accompanied by a reduced ability to infect Escherichia coli … One might logically conclude, therefore, that adaptation to a novel host–a host that is not infectible by the wild-type virus–should often produce an evolved virus that no longer infects the ancestral host, so that the host ranges of the closely related wild-type and evolved viruses no longer overlap.

(My emphasis.)

The model virus here is bacteriophage φ6. (I don’t know much about the phages, which is probably one reason I’ve missed out on the history of this work.) φ6 normally infects various Pseudomonas spp.For this work, they  started with a phage variant with a broad host specificity and used it to infect P. pseudoalcaligenes, which is not a normal host for the phage. They grew the phage for about 150 generations on this host, and then tested for host specificity, arguing that host specificity would not be directly selected, but (if it occurred) would have to be a side-effect of adapting to the host. That was indeed what they saw:

Thus, in all three populations showing reduced host range (increased host specificity), the phenomenon was caused indirectly by a single mutation that conferred a selective advantage on the novel host P. pseudoalcaligenes (increased host performance). … in φ6 assortative mating (host range) and ecological adaptation (performance on the novel host) had a shared genetic basis. … assortative mating evolved via a biologically simple “no-gene” mechanism in which assortative mating arises as a pleiotropic effect of mutations that produce ecological adaptation.

Vaccine-strain (MVA) vaccinia budding from chicken cells(My emphasis again)

I wonder what other aspects of a virus are involved. Are different kinds of virus (RNA vs. DNA, large vs. small, something else?) more or less likely to become host adapted/host restricted? This may seem like an academic question, but in fact I think it has a lot of clinical relevance. Apart from the question of emerging viruses and how they leap from one ecological niche (i.e. host) to a new one (i.e. us), there’s also a vaccine counterpart.

One of the traditional, and very effective, ways of developing a viral vaccine is to culture it on cells from an abnormal host — chicken cells, for example, for a human virus. In the process of adapting to the new host cells, the virus often loses virulence for the original host, and becomes a safe vaccine. I don’t know if there’s any kind of formal theory underlying this process or if it’s mostly empirical; this work may eventually lead to a more defined and rationale approach to developing safe vaccines that have less chance of reverting back to virulence in humans.


  1. Duffy, S., Burch, C.L., Turner, P.E. (2007). Evolution of Host Specificity Drives Reproductive Isolation Among RNA Viruses. Evolution, 61(11), 2614-2622. DOI: 10.1111/j.1558-5646.2007.00226.x []
  2. Ebert, D. 2000. Experimental evidence for rapid parasite adaptation and its consequences for the evolution of virulence. Pp. 163-184 in R. Poulin, S. Morand, and A. Skorping, eds. Evolutionary biology of host-parasite relationships: theory meets reality. Elsevier Science, Amsterdam.
    Fenner, F., and J. Cairns. 1959. Variation in virulence in relation to adaptation to new hosts. Pp. 225-249 in F. M. Burnet, and W. M. Stanley, eds. The viruses: biochemical, biological and biophysical properties. Academic Press, New York.[]