Brandon Keim at WiredScience has a new article on swine flu genomics.

“This is what we call a reassortment between two currently circulating pig flu viruses,” said Andrew Rambaut, a University of Edinburgh viral geneticist. “Why it’s emerged in humans is anyone’s guess. It hasn’t been seen before in pigs as far as I know.”


“The new neuraminidase gene that came in from Eurasian swine is one we’ve never before seen circulating in humans,” said Rambaut. “That’s one of the reasons it’s spreading rapidly. Very few people will have any immunity to this particular combination, which is what gives the concern that this will be a pandemic rather than just a normal seasonal flu outbreak. It remains to be seen how much and to what extent there is existing immunity.”

Story still evolving…Keim does mention that “a document released to scientists and obtained by affirms their analysis.” Could be out in the literature soon, possibly?

I was hoping to have a post up today with more thoughts on the whole pig issue, but no time to do anything but quick posts. Hopefully tomorrow…


  1. #1 PZ
    April 29, 2009

    MSN is still reporting the Avian,swine human genome link, accoriding to them some CDC expert was quoted; A brand new virus’
    Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, testified before a Senate subcommittee Tuesday that this hybrid flu — with pig, bird and human genetic components — has “pandemic potential.”

    “This is a brand new virus that we’ve never seen before,” he said. ” But what we’re focusing on is to contain the spread of this.”

    my question is is this new or is this the same as Ohio–trying to make sense of all the information is proving difficult.

    by the way a local school in the centeral valley were I live has just been shut down.

  2. #2 Tara C. Smith
    April 29, 2009

    Sandy’s updated her post saying additional analyses aren’t as suggestive of the Ohio strain being as closely related. I’m trying to sort it out too–as I mentioned in the other post, most (all?) currently circulating swine H1N1 strains are already a pig/human/avian mix, so I’m not sure if that’s where that came from, or not. I wish the CDC or someone else would put up some of their analyses on how they came to that conclusion…

  3. #3 eddie
    April 29, 2009

    PZ’s spelling, grammar are usually better than that.

  4. #4 ACW
    April 29, 2009

    This flu outbreak has prompted me to learn more about Influenza A, which is a fascinating organism regardless of how scared I should be of it. Learning about IA’s genome of eight negative-sense RNA strands prompts the following question.

    Do biologists know anything about how a new virion “musters” copies of the eight strands it needs to go forth and multiply? Is there a “collector” of some sort with slots that fit each of the strands? How does the virus guard against going out into the world with the wrong assortment of strands?

    (Also: eleven genes packed into eight boxes … three of the eight strands supporting multiple reading-frames … it’s pretty impressive!)

  5. #5 Arkady
    April 29, 2009

    ACW, how multi-segment RNA viruses package a complete genome is an interesting question and one that virologists have been investigating for quite a while. If i remember my final-year undergrad lectures rightly, the number of infectious virus particles is higher than would be expected if the genome segments were packed by chance alone (which would still have been a possibility, the ‘simplicity’ of many viruses means that some produce a lot of duff virus particles that are incapable of infecting a new cell), so there’s likely some packaging signals in the sequences. Been a while since i studied ‘flu in any detail tho, and we didn’t really do more than skim the surface on the subject.

  6. #6 Jared Cormier
    April 29, 2009

    I suspected this, avian and human elements probably from the American strain; Louisiana has 5 possible cases, the school was shut down

  7. #7 Heraclides
    April 30, 2009
  8. #8 BioinfoTools
    April 30, 2009


    While Sandy’s questions are good, I’d personally wait for more sophisticated analyses than Sandy’s initial efforts.

    I think her earlier demos of “bioinformatics lite” for newbies are fine, and she has a useful starting point, but I think her current analysis has too may weak points as a serious analysis. (Nothing against you personally, Sandy!)

    (The commentary in her thread seems to be bearing out my thoughts.)

  9. #9 Farouche Ombre
    May 2, 2009

    Heres some more hypebole…
    Neurospora crassa dose not have an activating compound and is either non-specific or their specificity has not been analyzed yet… but evolved as an adenovirus referred to as parvovirus that could be ascribed to Neu- by inference Adeno-associated virus of the host cell H1 to enable the virus to evade this designed mimetic defense… by an ontological tolerant time stamp identity can open that NS1 NCBI type Fasta edit window.

  10. #10 msn nick
    May 7, 2009


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