Back in 2007, I wrote about an outbreak of swine influenza from an Ohio county fair. The peer-reviewed paper analyzing the swine influenza isolated from that outbreak has just recently come out. From the abstract:

The swine isolate, A/SW/OH/511445/2007 (OH07), was evaluated in an experimental challenge and transmission study reported here. Our results indicate that the OH07 virus was pathogenic in pigs, was transmissible among pigs, and failed to cross-react with many swine H1 anti-sera. Naturally exposed pigs shed virus as early as 3 days and as long as 7 days after contact with experimentally infected pigs. This suggests there was opportunity for exposure of people handling the pigs at the fair. The molecular analysis of the OH07 isolates demonstrated that the eight gene segments were similar to those of currently circulating triple reassortant swine influenza viruses. However, numerous nucleotide changes leading to amino acid changes were demonstrated in the HA gene and throughout the genome as compared to contemporary swine viruses in the same genetic cluster. It remains unknown if any of the amino acid changes were related to the ability of this virus to infect people. The characteristics of the OH07 virus in our pig experimental model as well as the documented human transmission warrant close monitoring of the spread of this virus in pig and human populations.

Meanwhile, I mentioned yesterday that gene sequences from the new H1N1 virus had been released. Sandy has taken a look at some of these, and compared them with H1N1 and H1N2 viruses from humans and pigs.

Yes, there is a point to the juxtaposition of these two points, and it’s big–after the jump…

According to her analyses, the Ohio pig isolates are the most closely related to the new Texas and California human isolates. [Note: see comments in Sandy’s post regarding methods and other sequences also; expecting an update later today on her methods etc.]

Does this mean the virus came from these Ohio pigs? *Well, no, not necessarily*. First, we’re missing a lot of data. The sequences from any patients from Mexico still aren’t up (as of this posting), and we don’t have sequence information from Mexican pigs. Ideally, it would be very helpful to have not only data from pigs in the outbreak areas of Mexico, but multiple sequences over time, to see if this isolate was circulating there, had been recently introduced, had showed up in people, etc. However, that’s a lot of wishful thinking–more on this tomorrow. For now, this is a pretty big find.

I also assume this is where the human-avian-swine reassortant claim came from. The authors note that:

The H1N1 viruses contain the HA and NA from the classical swine virus and the internal genes from the triple reassortant H3N2 viruses (rH1N1); the H1N2 viruses contain the HA from the classical swine virus and the NA and internal genes from the triple reassortant H3N2 viruses (Karasin et al., 2002; Webby et al., 2004). Contemporary triple reassortant viruses were demonstrated to have acquired a PB1 gene of human virus origin; PA and PB2 genes of avian virus origin; and the remaining internal genes, M, NS, and NP, of swine virus origin, thus giving rise to the triple reassortant designation (Zhou et al., 1999).

So what it looks like to me is that this isn’t a *new* reassortant virus, but is closely related to one that had already been identified in swine–and that had already caused an outbreak in humans right here in the US.

I’ll have more about this tomorrow…this is pretty huge and I’m still digesting it all and looking for additional analyses…

[Update: additional analysis didn’t find what Sandy did using a different method, here…still developing…]


  1. #1 Jill U Adams
    April 28, 2009

    Does this mean it’s possible we’ve had Ohio swine flu in the US for awhile? And it’s just getting attention now because of the deaths in Mexico (from a different — or a more recently mutated — strain)?

  2. #2 Sandra Porter
    April 29, 2009

    Thanks Tara!

    This is great. Your insights put it all together.

  3. #3 Mark O. Martin
    April 29, 2009

    So I read things like this:

    And then I wonder: is my paranoia detector working correctly, or not? The stories sound pretty dramatic.

    How do they sound to you?

  4. #4 Ian
    April 29, 2009

    I’m sorry everyone around here seems to be trumpeting Effect Measure for swine flu info. They’re good but they’re not you! Keep the info coming.

  5. #5 eddie
    April 29, 2009

    Unconfirmed report from NASA suggests that mexican flu has extra-terrestrial origin;

  6. #6 chuck
    April 29, 2009

    Would the “Ohio flu” explain why this one (so far) has been more severe in Mexico than here?

  7. #7 Brian Foley
    April 29, 2009

    The H1:N1 flu viruses in this current Mexico/USA/world epidemic are not significantly more related to the 2007 Ohio swine flu cases, than they are to viruses from H1:N1 and H1:N2 swine flu viruses found all over the world over the past 20 years. Yes, the OHIO fair viruses were H1:N1, but so are many swine viruses found all over the world.

    It is way jumping the gun, to attempt to pinpoint an origin or origins for the virus(es) involved in the current human cases. There are millions or billions of pigs on earth, and we sample a few hundred each year for sequencing the viruses. Same for the birds.

  8. #8 J A Ginsburg
    April 29, 2009

    This is stunning Tara. Combined with studies showing a spike in the number of swine flu strains over the last decade and a 2007 study (using 2006 sample) identifying a naturally occurring swine/avian mix (, it seems like we shouldn’t be all that surprised this is happening.

  9. #9 Ron
    April 29, 2009

    Hi Tara,
    Everyone, from Smithfield to the Mexican health authorities, are denying that pigs actually have anything to do with this epidemic, ie H1N1 has been circulating among humans for quite a while (Didn’t pigs get it from us?). No detection of sick pigs nor sick pig farm workers. Yet you seem to be tracing the origins to pigs.

    Could one reason nothing has been detected in pigs the fact that pigs in big farms are universally vaccinated for H1N1, thus masking low levels presence of the disease?

    As to reports from Mexico, it seems to me that what is happening is panic, primarily due to incredibly poor official communication about the true situation. Mexicans due not trust their government, with good reason.

  10. #10 AJ
    April 29, 2009

    Ron, not all pigs are vaccinated. You need to consider organic-raised pigs and ABF hogs.

  11. #11 Ron
    April 29, 2009

    AJ, I was referring to large industrial pig farms, like the Smithfield plant near Perote Veracruz, where the first case of H1N1 appeared in a child. (he recovered). They vaccinate and no flu has been detected in animals or workers.

  12. #12 Firing Squid
    April 30, 2009

    Good on you, Tara, you are answering possibly the most important question in this entire incident.

  13. #13 Maeva
    May 1, 2009

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  14. #14 jedati
    May 1, 2009

    I live in Indiana and my daughters mother in law is a nurse in Greencastle. A few months ago she said the flu was horrible there because her patients had so much vomiting and diarrhea. Now I am reading that the flu that typically goes around does not have so much of that, but this swine flu does. I am wondering if this has been around for a while and no one was testing the right people????

  15. #15 Helper
    May 4, 2009

    We will get more unknown deceases. There is a free book that talks about all this. It says that since 2001, we will get more of these besides hurricanes, tsunamis, earthquakes, floods etc. You can request it at You do not need to join a group or money. The book is a gift for humanity as the last resource to help it through the coming years. The only catch is that you must do the practices in the book. Any human being regardless of color, race, religion, poor, rich etc., has within has is necessary to overcome what is coming in any place of the planet. Good luck!

  16. #16 lonik
    May 5, 2009

    This website shows you in real time how quickly swine flu is spreading.

  17. #17 GM
    May 5, 2009

    Has anyone read this?
    Research Indicates Eco-Safe Ozone Disinfection Would Inactivate Type A, H1N1 Virus

    On Tuesday May 5, 2009, 6:00 am EDT
    Buzz up! Print LOS ANGELES, CA–(MARKET WIRE)–May 5, 2009 — Eco-Safe Systems USA, Inc. (Other OTC:ESFS.PK – News) deems it significant to emphasize research published in July 2008.

    A study completed by researchers at the Mayo Clinic, Brigham Young University, and Utah Valley State College was published by the Journal of Virological Methods which documented the inactivation of a Type A, H1N1 virus by ozone disinfection. The virus responsible for the current outbreaks of Swine Flu is classified as a Type A, H1N1 virus.

    Michael Elliot, President of Eco-Safe, said, “Public health concerns for the spread of viral illness in schools, restaurants, and other venues are of prime consideration by Eco-Safe. Proper disinfection of food, utensils, and food service workers’ hands has become an absolute necessity in light of the current public health emergency of Swine Flu. Ozone disinfection is the strongest, fastest, safest, and a completely green method for reliable disinfection of known pathogens.”

    Larry LaVerne, Eco-Safe Director of Marketing, added, “Several Eco-Safe clients who process seafood have given us anecdotal reports of reduced employee illness after installing Eco-Safe Ozone Disinfection in their businesses, with one distributor reporting 60% fewer employee sick days. When you reduce the load on the immune system, the infection rate goes down.”

    About Eco-Safe Systems:

    Eco-Safe Systems, based in Los Angeles, is the manufacturer of patent pending water treatment and water reclamation systems. Our technologies produce ozonated water for food disinfection and water purification at significantly less maintenance cost and greater energy savings than our competitors in a completely green and organic manner. Please visit us at for more information.

    The foregoing contains forward-looking information within the meaning of The Private Securities Litigation Act of 1995. Such forward-looking statements involve certain risks and uncertainties. The actual results may differ materially from such forward-looking statements. The company does not undertake to publicly update or revise its forward-looking statements even if experience or future changes make it clear that any projected results (expressed or implied) will not be realized.

  18. #18 Swine Ful Facts
    May 7, 2009

    I just cannot understand why they blame humans and not pigs for spreading this disease to all over the world. Humans first, destroy all pigs.

  19. #19 siirt
    May 8, 2009

    Siirt hakkında güncel haberler sunan yerel haber sitesi

  20. #20 silah oyunlari
    May 12, 2009

    And then I wonder: is my paranoia detector working correctly, or not? The stories sound pretty dramatic.

    How do they sound to you?

  21. #21 TalkSwineFlu
    May 16, 2009

    I think the vaccine should be produce already because the Swine Flu could pickup again and who knows could be worst when it comes back.

  22. #22 Paul Heikkila
    June 4, 2009

    China is reportedly expecting to produce vaccine for A/H1N1 as early as late July.

    In the US we do not expect to see vaccine until October. The usual explanation for the delay is that the production process involves growing the vaccine in eggs which takes several months. What is it we are seeing in China? More efficient production? A new way of producing vaccine? A poor translation of what was really said?

  23. #23 Micheal
    June 18, 2009

    South Africa’s first swine flu case – a 12-year-old boy who flew in from the US – has been confirmed.

  24. #24 Paul H
    July 7, 2009

    Is “virility” a term still applied to flus? You’d think that would have been selected against decades ago. No doubt a virile flu took out the Duke and Norman Mailer. Dick Cheney prays for one to take him out, but we know it will be some “pansy” flu that gets him in the end.

  25. #25 Jeff
    November 10, 2009

    I realize I’m a little late to the party but wanted to mention the CDC website is now calling it a quadruple reassortant (see They state it has two genes from flu viruses that normally circulate in pigs in Europe and Asia and bird (avian) genes and human genes.

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