Increased fidelity reduces viral fitness

15 May 2009

pvrtgWe have spent over a week discussing the effects of polymerase error rates on viruses. RNA viruses have the highest error rates in nature, a property that is believed to benefit the viral population. For example, selective pressure from the immune system or antiviral drugs may lead to changes that are beneficial for the population. In fact, it has been hypothesized that high error rates are required for survival of RNA viruses in complex environments. The isolation of a poliovirus mutant with an RNA polymerase that makes fewer errors during replication made it possible to test this hypothesis.

Infection of an animal host poses perhaps the greatest challenges to viral propagation. Transmission, entry, host defenses, tissue diversity and anatomical restrictions all are serious obstacles to the ability of a virus to replicate, disseminate, and successfully spread to other hosts. Therefore the effect of viral diversity is most stringently tested in infection of an animal.

In these experiments, mice were inoculated with the poliovirus mutant containing the G64S amino acid change in the viral RNA polymerase that causes enhanced fidelity. Infection of mice with poliovirus typically leads to symptoms of poliomyelitis that are similar to those in humans. Compared with the wild-type parental virus, the G64S mutant was less pathogenic: it caused significantly less paralysis and lethality. This effect could be a consequence of restricting the viral quasispecies, or a replication defect in mice caused by the G64S mutation. To distinguish between these possibilities, the G64S mutant was propagated in cells in the presence of a mutagen, a procedure which expanded the number of viral mutants. This treatment – basically expanding the quasispecies – lead to a significant increase in lethality of the G64S virus, to nearly the same extent as wild type virus.

Why would a less complex quasispecies lead to reduced pathogenicity? Viral growth and spread in an animal likely requires a diverse viral population, comprising many mutants, which can replicate efficiently in the many different cell types in an animal. Support for this idea comes from a competition experiment in which the poliovirus G64S mutant was mixed with wild type virus and inoculated into the leg muscle of a mouse. Several days later the mice were sacrificed and the virus that had reached the brain was characterized.  The results showed that both wild type and the G64S virus could replicate in muscle, but the mutant virus spread to the brain less frequently.

These results show that mutations do benefit viral populations, especially in complex environments such as an animal. The ability to produce a quasispecies may allow virus populations to respond to the different environments encountered during spread between hosts, within organs and tissues, and in response to the pressure of the host immune response.

We’ll shortly return to influenza virus replication, but I hope you have been able to follow what to many must be a somewhat arcane discussion. From the silence I suspect that I might have lost some of you – it might help to go back over some of the posts. I’ll try to put up an index of some sort to make it easier to find articles. The blog format isn’t great when it comes to finding older material – once posts scroll off the bottom of the page, they don’t receive further notice.

Pfeiffer, J., & Kirkegaard, K. (2005). Increased fidelity reduces poliovirus fitness and virulence under selective pressure in mice PLoS Pathogens, 1 (2) DOI: 10.1371/journal.ppat.0010011

Vignuzzi, M., Stone, J., Arnold, J., Cameron, C., & Andino, R. (2005). Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population Nature, 439 (7074), 344-348 DOI: 10.1038/nature04388

  • http://www.chicagotribune.com/ Trine

    I was sitting on the train tonight across from a woman who was hacking up a lung. I think I spotted beads of sweat on her brow. Fever. Pondering how quickly I would fall sick with her horrible illness (swine flu?), I wondered, have human beings developed any kind of immune defense that reduces viral RNA errors, or increases them? And if not, why not? It would seem like a great immune defense. Or maybe not.

    Feeling the viruses replicating in my respiratory epithelial cells already (it's been almost two hours),

    T

  • http://www.chicagotribune.com/ Trine

    By the way, this discussion of quasispecies has been fascinating, not arcane. I've been knee-deep in a project story all week, but finally am up for air and found the whole thing interesting. T

  • OleDocJ

    I've enjoyed your presentation on this topic. It is indeed a difficult topic for many (say, non-virologists) to get a handle on. You've done a good job. I've followed this area since my days in the Holland lab (almost 40 yrs ago!). I appreciate how difficult it is to simplify.

    My analogy is that it is like explaining quantum vs Newtonian physics: quasispecies virology involves nonlinear thinking (like quantum) whereas thinking in terms of virus genes and gene sequences involves linear thinking (Newtonian). It's a bit of a juggling act that takes time and practice (repetition) to do!

    Thanks for the good read!

  • http://www.virology.ws profvrr

    Glad you enjoyed it, and that it was clear. It all started in the Holland lab, as I'm sure you know.

  • http://www.virology.ws profvrr

    What a terrific idea, to reduce viral errors as a means of defense. I don't know of any such defense but it makes perfect sense. And shows me you have been understanding the posts.

    We live and prosper in a literal cloud of viruses….our immune systems are generally excellent at preventing most infections. You are attuned to viruses by virtue of your work, but chances are you will be fine. When swine flu first broke out, I was on the subway, holding the greasy pole, and washed my hands immediately afterwards. I would never have done that before – just goes to show how we get more aware of viruses when we are hearing about them all the time.

  • http://www.linkedin.com/in/jasonjens Jason Jens

    I'm so glad to see that there is good research supporting an idea I've always thought might be the case. My appreciation extends to you for grasping and communicating the true nature of “natural selection” and the inherent complications in predicting it. To anyone who's ever written a genetic algorithm, the preservation of diversity is a well-known requirement for multiple unique solution-finding. An interesting, conflicting selective pressure would be for a robust genome. If you are going to allow (indeed encourage) an error-prone replication system, then your genome must have a sufficient level of robustness to resist throwing the whole infection process out-of-whack. (Excuse the personification) In an undergraduate thesis, I mused about the error rates of polymerases as an argument against the simplified, teleological theories extended by 20th century evolutionary biologists. It's good to see research that agrees.

  • http://www.linkedin.com/in/jasonjens Jason Jens

    This has been thought of already for bacterial infections. see…

    http://www.pubmedcentral.nih.gov/articlerender….

    Turns out SOS response in bacteria turns on mechanisms to become error-prone at self-replication. Dam dirty defense-mechanisms! Bacteria and viruses are always one step ahead, aren't they!?

  • phytosleuth

    You haven't lost me totally. I am behind in reading posts, but they will be there. I get the gist of the most recent post. And the defense mechanism of reducing viral errors has me wanting to go on a search to see if plants use this defense mechanism. Anyone know offhand? Would save me a search…haha..

  • Matt Dubuque

    Great stuff! Keep up the wonderful work!

  • Matt Dubuque

    I did my undergrad work studying under British naturalist/epistemologist Gregory Bateson, whose father William Bateson first coined the word genetics after translating Mendel's work from the original German.

    This association of genetic diversity with enhanced survival of viral quasispecies reminds me of discussions we used to have about these concepts on a much large scale.

    Bateson's lectures were replete with examples of coevolution, where the strategies of the pollinator coevolve jointly with the strategies of the flower, where the strategies of the predator coevolve jointly with the strategies of the prey, etc., each coevolutionary example comprising an array of mutually interacting feedback loops over time.

    And Bateson's inference from the myriad examples of coevolution in the natural world was that, by logical extension, human produced monoculture environments (corporate agriculture for example) are necessarily less adaptive due to their loss of ecosystem diversity.

    Personally, I can see some nice formal parallels between those discussions and the modulation of “variation rates” in viral replication to find that “sweet spot” of viability over time.

  • http://www.linkedin.com/in/jasonjens Jason Jens

    Human agriculture is indeed an interesting case-study in evolution and how artificial selection has affected it/been affected by it. There are some great theories and observations from paleobiology and biogeography precipitated in GUNS, GERMS, AND STEEL (by Jared Diamond) regarding the choices of culturable grains, fruits, vegetables, etc. made by early human societies. I would highly recommend it for any interested parties.

  • Matt Dubuque

    Thanks Jason, I'll be sure to read that Pulitzer Prize winner of his.

    I thought his book “Collapse” was a compelling read. I hope to interview him for my film “100 Trees”

    http://www.youtube.com/watch?v=_dPUp1m1pLA

  • Matt Dubuque

    In terms of plants doing this, I would think that the interplay between tobacco and tobacco mosaic virus would be a plausible candidate for a paper or three. But I can't speak as to whether this particular defense mechanism was addressed.

    A post here a few weeks ago mentioned a plant (I don't remember the name) which had diluted and mild antiviral properties. It might be interesting to see what particular mechanism was present there also.

  • ET

    Guns Germs and Steel was also a three-part PBS series. Naturally, never as much detail as the book, but PBS did an admirable summation.

  • Matt Dubuque

    Thanks ET. That is now next in line in the Netflix queue.

  • http://masseybioinformatics.uprrp.edu/ Massey

    If reduced fidelity is beneficial to RNA viruses, because of the complex environment they are in, why don't DNA viruses do the same thing?

  • http://www.virology.ws profvrr

    That is a fascinating story. Thanks for pointing it out. It's easy for
    bacteria and viruses to stay one step ahead, because they evolve so
    quickly. Fast generation times + high yields of offspring + error
    prone replication = rapid evolution.

  • http://www.virology.ws profvrr

    Why should all organisms evolve to the same end point? DNA viruses
    evolved to have larger genomes; perhaps they compensate for reduced
    diversity with far more gene products with which to modulate their
    interaction with the host.

  • Frank

    I would like to contribute to this discussion about fidelity and fitness. I have read the article you are refering to and i agree, that a low fidelity at genome replication contributes to survival and adaptation of a virus to a new host.

    BUT i would like to emphazise this point : as Pfeiffer et al. have shown, a polio mutant displaying lower fidelity in genome replication isn`t able to adapt very fast to the “new” host (mice in this case). This goes hand in hand with a reduced pathogenicity or a later onset of severe symptoms.
    But why would that be -as it is described here – a disadvantage to the virus? I don`t like to speak of “aims”, as evolution and organisms such as viruses (to my understanding) don`t have “aims”, but to clarify my point : isn`t it the “aim” of a virus to survive, replicate and spread? Maybe the virus with a polymerase showing higher fidelity can`t adapt easily to different “enviroments” within the host, but nevertheless, it still replicates and importantly it doesn`t kill its host (at least not as fast as a wt virus does). Therefore, the host would be able to shed the virus over a prolonged time (again compared to the wildtype) which means the virus with “lower” fitness is able to spread more efficiently within a population of animals/hosts.

    To summerize my thougths : higher fidelity -> lower pathogenicity -> host survives for a longer time -> virus can spread more efficiently within a population.

    I don`t want to rule out the benefit of a high mutation rate, but to me it is important to mention that -in my opinion- there has to be a kind of an “equilibrium” between easy adaptation and fast replication within a host (caused by high mutation rates) and the fact, that the virus “wants” to spread, which is easier, if the host survives longer.

    I would be very glad about answers to this post and a discussion about this comment.

    Frank

    P.S. : This Blog is really a great thing. It`s good to see that people sometime come “out” of their fields to view virology on a kind of larger scale.

  • http://www.virology.ws profvrr

    If this were the case, then all viruses would evolve to be highly
    transmissible and of low virulence. But this is certainly not the
    case. There must be some advantage of higher virulence that we don't
    understand. To consider your other point, viruses with higher fidelity
    cannot compete with viruses that make more errors. Plus, the higher
    fidelity virus is eliminated because it cannot evade host responses.

  • http://www.virology.ws profvrr

    If this were the case, then all viruses would evolve to be highly
    transmissible and of low virulence. But this is certainly not the
    case. There must be some advantage of higher virulence that we don't
    understand. To consider your other point, viruses with higher fidelity
    cannot compete with viruses that make more errors. Plus, the higher
    fidelity virus is eliminated because it cannot evade host responses.

  • Liam Thompson

    Apologies for being 2 years late, I’m not sure how I got here. I was hoping you have more insight on the advantage of higher virulence. I was quite convinced from colleagues that HIV was becoming less virulent. Does the differing virulence of viruses have to do with those continuously circulating in the population on a large scale (HIV, HCV, HBV and HPV) as opposed to those that do not which are seasonally or intermittently introduced ? (@Massey) HBV is an example of a DNA virus with a small genome (3.2kb), and a error rate 96% of HIV. Do you think it’s outlier status is due to it’s overlapping genome ?