An analysis of “The early diversification of influenza A/H1N1pdm” paper

A paper has recently appeared in PLoS Currents describing the evolution of the pandemic H1N1 virus. It was written by Martha Nelson, David Spiro and David Wentworth. Samples were collected in New York and Wisconsin and sequenced at the J. Craig Venter Institute.  The dataset included these sequences as well as the pandemic H1N1 sequences which have been deposited in GenBank. Sequences from GISAID were not included, presumably due to their restrictive policies on data analysis.

Influenza viruses mutate frequently. Despite some erroneous press reports, this applies to pandemic H1N1 just as much, if not more, than seasonal flu. In the PLoS paper, statistical techniques were applied to the sequence dataset described above to separate out the various pandemic flu isolates into 7 distinct groups called clades. The sequences contained within each clade are more closely related to each other than to the other clades. However, they are not necessarily identical. The paper describes the relationships between the different clades and outlines their geographical distribution.

One of the most striking results from this paper was that although six of the seven clades were found in multiple regions throughout the world, in the two areas that were extensively sampled, New York and Wisconsin, there was a clear founder effect. In other words, most of the people in each area were infected with the descendants of specific strains of virus. Most people in Wisconsin were infected with a different variant of the virus than most people in New York were infected with.

Although the authors of the PLoS Currents paper did not demonstrate any obviously functionally important changes in pandemic H1N1, they did clearly show that the virus is mutating and diversifying as it spreads. Further, they found that regionally distinct clades are evolving in different geographical areas. Since the sort of intensive sampling and sequencing conducted for this paper is rarely done, we can only guess at how the virus is evolving in thousands of regions around the world.

Although the WHO and the CDC frequently suggest that the pandemic H1N1 virus is an homogeneous entity, the reality is quite different. The virus is opening many different doors, simultaneously. We don’t know what the odds are that one of these doors will lead to higher virulence or Tamiflu resistance. But what we do know is that it will keep opening door after door, in city after city, month after month in a never ending search for optimal fitness.

Nelson et al. (2009) The early diversification of influenza A/H1N1pdm. PLoS Currents.


4 thoughts on “An analysis of “The early diversification of influenza A/H1N1pdm” paper

  1. “describing the evolution of the pandemic H1N1 virus.”

    What is a pandemic? Is it as the prefix “pan” suggest, all encompassing? Many people hear these terms and assume total destruction.

    Bottom line–at some point our species will be strengthened by weeding out the weak (immunologically). Until then we are avoiding the inevitable. Penicillin may have delayed this affect but did not eliminate it.

    Do I suggest avoiding medical care? No, but I suggest we don’t become consumed by things beyond our control.

  2. pelagian7, what makes you think you are not among “the weak”? Why stop at antibiotics? Shouldn’t you refrain from clean water, central heating and all the other fruits of human ingenuity? Heck, you should give up on fire and the wheel too, don’t you think? Surely all of these protect “the weak”. Then, you can hunt deer and fight off mountain lions, without even a sharpened stick. If you can do that, then you can claim not to be among “the weak.”

    Me, I prefer to be among “the intelligent” than “the strong”. It was brains that made our species successful not immunological luck. But to each their own.

  3. You are misunderstanding my thread.

    My points are:
    *Humans will suffer a pandemic, we are over-populated and our close proximity will assure wide spread infection.

    *Millions died of flu in the early 1900’s. Today’s H1N1 is not pandemic in its current form, but is hyped as such for political and commercial benefits.

    *Science and research are my passion, yet, we will be weeded out (immunologically) at some point. If intelligence is as important to you as you say, then you should know the experts are not saying if, but when will the next plague happen.

    *Your response, {pelagian7, what makes you think you are not among “the weak”? Why stop at antibiotics? Shouldn’t you refrain from clean water, central heating and all the other fruits of human ingenuity? Heck, you should give up on fire and the wheel too, don’t you think?}
    *This is non responsive to anything I said. You are making assumptions and showing your own ignorance.

    *Finally, strength or weakness were only referred to as in susceptibility. And although brains were a major factor in our success the immunologically unlucky, may have had great intellect, but died anyways, as we all do.

  4. pelagian7, what do your posts have to do with the subject of this blog, namely the paper published in PLoS Currents? Because they look kind of non-responsive, to me. More like generic pandemic denialist rhetoric.

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