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More H5N1 Evolution via Recombination

Recombinomics Commentary

May 1, 2005

>> That tradeoff could occur through reassortment - a process in which an avian virus and either a human or a swine flu virus swap genetic material. But it could also occur through a series of small evolutionary steps, each of which makes the virus better equipped to survive in people.

'You get one good mutation which then sweeps through the population because all the viruses with that mutation grow better," Dr. Brown explains.

'And then you can get another mutation on top of that and maybe another gene which gives you a leg up and that sweeps through the population. And then those become the dominant viruses."

That may be the process that is occurring now.  <<

Neither of the above processes is driving the genetic changes in H5N1.  They represent the two pillars of influenza genetics that have never made much sense, and the H5N1 evolution should have made that very clear by now.  However, the same old explanations are trotted out followed by a "we don't understand".

H5N1 evolves via recombination.  The H5N1 in Hong Kong in 1997 had 8 avian genes.  The H5N1 in 2003 in Hong Kong had 8 avian genes.  The H5N1 in Vietnam and Thailand in 2004 had 8 avian genes.  The H5N1 in 2005 in Vietnam and Cambodia had 8 avian genes.  The H5N1 in northern Vietnam in 2005 had 8 avian genes.  H5N1 has been evolving, expanding its host range, and changing its lethality with 8 avian genes.  No human genes. No swine genes.  No reassortment.

The old mutation story to explain rapid change is also nonsense.  The H5N1 has been gradually changing, but it has done so by shuffling polymorphisms via recombination.  New polymorphisms are due to mutation, but H5N1 doesn't use new mutations for rapid change,  it recombines to acquire old polymorphisms.

The dropped amino acid has been brought up to explain the more efficient transmission and lowered case fatality rate.  This missing amino acid is almost certainly a basic amino acid at the HA cleavage site, and it almost certainly is an exact match of the missing basic amino acid in H5N1 isolates from China in 2003.  The change in northern Vietnam in 2005 is not due to a new mutation, but the acquisition of an old mutation via recombination.

H5N1 is evolving via recombination, not reassortment or mutation.  It is time for some of the WHO consultants to turn in their membership cards in the "Flat Earth Society", and move on to a true understanding of how influenza evolves.

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