Swine influenza A/Mexico/2009 (H1N1) update

1 May 2009

reassortment-swineHere is an update on the global swine flu situation as of 29 April 2009.

There are now 257 laboratory confirmed cases, with 7 deaths, in 11 countries. In the US there are 109 cases  in 11 states. There are many more suspected cases; together the statistics indicate widespread dissemination of the new H1N1 influenza virus. I no longer doubt that this is the next pandemic strain. WHO will probably soon raise the level of influenza pandemic alert from phase 5 to phase 6. Important questions include whether spread will continue in the northern hemisphere through the summer, or stop very soon, as is the case with most influenza virus outbreaks. Unfortunately the southern hemisphere seems in for an extended flu season. Will antivirals be useful in reducing morbidity and mortality? Will the virus returns to the north in a more virulent form in the fall? Can a vaccine be prepared in time?

Viral RNA sequences from 12 new isolates were deposited at NCBI, bringing the total to 32. Conspicuously missing are sequences from Mexican isolates. In a Science Magazine interview, Ruben Donis, Chief of the molecular virology and vaccines branch at CDC, indicated that strains from Mexico and elsewhere are “very, very similar. Many genes are identical. In the eight or nine viruses we’ve sequenced, there is nothing different.” It’s still not clear why these sequences have not been released; clearly the work has been done. In any case, his statement confirms what we have suspected from examining other isolates, that the Mexican strains are not sufficiently different to explain their apparent higher pathogenicity.

I highly recommend reading the interview with Dr. Donis, as it contains a wealth of information about the new H1N1 virus. Much of it will be difficult to understand for those without familiarity with influenza virus, but you can send your questions to virology blog. One interesting aspect concerns the statement last week that the new virus was composed of genes from pig, human, and avian sources. Examination of the sequences in the past week has revealed the virus to be composed of RNAs solely from swine viruses. Here is what Dr. Donis said:

Q: Is it of swine origin?

R.D.: Definitely. It’s almost equidistant to swine viruses from the United States and Eurasia. And it’s a lonely branch there. It doesn’t have any close relatives.

Q: So where are avian and human sequences?

R.D.: We have to step back [to] 10 years ago. In 1998, actually, Chris Olsen is one of the first that saw it, and we saw the same in a virus from Nebraska and Richard Webby and Robert Webster in Memphis saw it, too. There were unprecedented outbreaks of influenza in the swine population. It was an H3.

The PB1 gene, that was human. H3 and N2 also were human. The PA and PB2, the two polymerase genes, were of avian flu. The rest were typical North American swine viruses. Those strains were the so-called triple reassortants.

I’ll post an entry this weekend on the history of swine viruses, which should help clarify Dr. Donis’ explanation.

On Friday, 1 May I will be holding a FAQ session on swine flu with Marc Pelletier of Futures in Biotech. A video stream of our conversation will be broadcast live at 4:00 PM EST at live.twit.tv. Send us your questions via twitter to @profvrr.

  • diana

    Dr. Racaniello,

    This confuses me:

    http://www.cdc.gov/mmwr/preview/mmwrhtml/mm58d0

    See note 1.

    “genetically similar to viruses subsequently isolated from patients in Mexico “

    Hunh?

    When you click on Note one, you get

    http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5816

    Which doesn't contain a reference to RNA sequences of Mexican cases. Unless I am misreading – which is possible.

  • Matt Dubuque

    At the end of the interview, Dr. Donis states that the USA has received 300 samples of this virus from Mexico.

    It seems to be a conscious and intentional decison not to publish those sequences.

    Why would the CDC fail to publish the sequences of any of the 300 samples Dr. Donis says they have received from Mexico?

    Matt Dubuque

  • bibi

    Hello,
    could anybody answer this:
    how comes that the current year's vaccin is not effectiv on the new “mexico ” H1N1 ?
    The H1N1 strain is used in vaccins since 2002 ( probalbly much longer before) ?
    thanks
    bibi

  • http://www.virology.ws profvrr

    Even though both viruses are H1N1, the Mexico isolate is very
    different from the previous H1N1 and therefore there is probably no
    cross-protection. So says the CDC, although no one has seen the data
    that would answer the question either way. I will ask Peter Palese
    this question next week on TWiV.

  • http://www.virology.ws profvrr

    You are right, it doesn't make sense. There is no reference to the
    statement about Mexican isolates. They clearly are not releasing these
    sequences.

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  • bibi

    Thank you – your blog is great – I can find this information no where and spent hours on pubmed
    I dont understand the terminology : how could two H1N1 strain be different ?
    Could you explain how vaccination works : when H1N1 strains are used to produce a vaccination why wouldn't they work on “other H1N1 ” strains ? ( Hapten has changed – but not enough to call it HxNx)?
    many thanks again:
    from europe
    bibi

  • http://www.biomed.emory.edu/PROGRAM_SITES/MMG/faculty.html Ruben Donis

    Thank you for the nice vignette about the ScienceInsider interview. I would like to point out that full genome sequences of Mexican viruses have been available in the public domain at the GISAID database http://www.gisaid.org since April 24, 2009. Sequences were posted in the public domain as soon as they were completed and curated. The availability of sequences at GISAID was also posted at the WHO website
    http://www.who.int/csr/disease/swineflu/swinefl

  • http://www.virology.ws profvrr

    Thank you Ruben for clarifying this. I just discovered the Mexican
    sequences today. I missed the WHO announcement about GISAID as did
    most readers of virology blog.

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  • teeess

    I'm supposed to take my students to a National Convention in Dallas in June (which was post phoned from May 6-9) . I'm afraid that Texas is too close to the border, and I don't want to be in a conference with over 5,000+ students, one of which could have just come over from Mexico. What are the chances this is all going to be over by June 17?

  • http://www.virology.ws profvrr

    New cases in Mexico appear to be rapidly declining
    (http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5817…). There is
    an excellent chance that it will all be done by June; it's very rare
    to have flu outbreaks in that month.

  • teeess

    I'm supposed to take my students to a National Convention in Dallas in June (which was post phoned from May 6-9) . I'm afraid that Texas is too close to the border, and I don't want to be in a conference with over 5,000+ students, one of which could have just come over from Mexico. What are the chances this is all going to be over by June 17?

  • http://www.virology.ws profvrr

    New cases in Mexico appear to be rapidly declining
    (http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5817…). There is
    an excellent chance that it will all be done by June; it's very rare
    to have flu outbreaks in that month.