Effect Measure

Flu in Vietnam — and wherever you live

What looked like probable human H5N1 in Vietnam with four cases in one family (a mother and three children), may not be, although the circumstances are sufficiently suspicious we prefer to suspend judgment a bit longer before concluding that this was a false alarm. False negatives and false positives occur. In some senses, though it doesn’t matter much. The virus continues to be found in poultry in more and more places in Vietnam, with 73% of poultry samples in the central province of Qung Nam reported positive. These developments are probably a combination of endemic virus, infected poultry smuggled in from China to meet the demands of the upcoming Tet holiday and possibly some role for migrating wild birds. Human and poultry cases follow a typical seasonal pattern of influenza, so we will likely see human and poultry cases as the season advances.

Why flu is seasonal, is a bit of a mystery. Various explanation have been given but none have been shown to explain the pattern to everyone’s satisfaction. We are also entering flu season for “ordinary” human influenza, and we took a look at the latest CDC report and found a bit of a surprise. The most recent report is from week 51 (the week before this one) and some of it is quite predictable. Using data from specimens tested by WHO and national reference laboratories in the US, we find four states with widespread influenza activity, 12 more with regional activity, 5 states with local activity, one state reporting no activity and 3 states who did not report. Here’s the map. You can see the widespread activity is in the southeast states:


Source: CDC weekly flu report

The big surprise (to me, anyway) was in the antigenic characterization of the circulating virus this season. Since 1968 H3N2 has been the dominant subtype but in 1977 it was joined by H1N1, which had been the principal subtype between 1918 and 1957. The usual circulating influenza A was H3, however. This year, almost all the typed influenza A virus has been H1. Only one isolate (in week 42) was H3. We should say that most of the viruses (77) were untyped, so it is almost certainly true that some of these were H3s, but the lopsided proportion (24 H1 versus 1 H3) in typed viruses is quite striking and unlike previous three years where H3 predominated, overwhelmingly. The strains in both cases matched the seed strains in the vaccine, so it doesn’t appear that the H1 predominance is vaccine strain mismatch.

With all the attention on H5N1, it is wise to remember that the greatest influenza danger at the moment is from the old stand-bys, influenza A subtypes H1N1 and H3N2 and influenza type B, the viruses responsible for “usual” seasonal influenza. What this seemingly unusual pattern of circulating H1N1 early in the season might mean (if anything) I don’t know, but it is curious. Influenza ramps up noticeably in January of most years, so there is still time to get a flu shot, which is well matched for these viruses.

While we struggle to understand what might spark a pandemic, we still have to contend with endemic influenza which itself is capable of explosive outbreaks that go beyond the seasonal baseline. In 1951 a seasonal H1N1 outbreak in Liverpool produced mortality there that exceeded that of the 1918 variant, so this virus is anything but benign, and we still don’t understand it.

While your eyes are on Vietnam and Indonesia, don’t forget what’s happening where you live.


  1. #1 mary in hawaii
    December 31, 2006

    Revere: Could you spend a moment reeducating some of us who might have forgotten what types of tests are done to determine if someone is infected with H5N1?

    In the case of these negatives from Indonesia, it seems like the test results were returned in record time. I do recall some data from WHO that states quite unequivocally that antibodies don’t show up to H5N1 until day 9 or 10 following infection. Per the news reports, the family entered the hospital only Dec 30, and had eaten the suspect chicken during “the week before”, which means only about 8 days had passed, max. In that case, the “negatives” couldn’t have been from antibody tests, but I’ve forgotten the specifics of what the rapid PCR tests look for, as compared with the later and – as I recall – more definitive antibody tests.


  2. #2 revere
    December 31, 2006

    MIH: Quick answer as it is getting on midnight and my presence is requested. Quick antigen tests (for presence of viral protein), not very sensitive especially with H5N1; meant to tell if influenza A or not. Viral isolation (grow virus in tissue culture), time consuming but “gold standard”; PCR tests for viral genetic material. All of these are for presence of the virus and don’t depend on antibodies developing to it. PCR is sensitive and specific if you have an adequate specimen to work with.

  3. #3 DeLuca
    January 1, 2007

    I am a healthcare provider and always get a yearly flu vaccine (including this year in October). I normally work in Philadelphia but have been in the outlying suburbs over the last two weeks. Last night I began to feel ill and I am nearly certain that I have influenza. Severe myalgia, lethargy, mild cough, sore throat and febrile. I have not had influenza since November 1996, which was significantly more incapacitating. I use hand sanitizer each time I enter the car and when I arrive home and practice excellent handwashing. It is frightening to consider that despite the care I took to avoid flu, it seems as if jas found me nonetheless…glad it’s not BF.

  4. #4 Jon "AmericanOz" Singleton
    January 1, 2007

    Mary, Happy ’07 to yourself and family… The other day you sent me a predictable AmericanOz Babyboomer email ie. “We hate you, so please frack off and die you 38 year old smartarse!” Yes, in your tres brief email, a singular lucid statement I’ve interpreted as “do I do any backgrounder reading before writing for an audience” stands out: Mary — “[Jon,] dO YOU EVER CHECK? CHECK!!” Well Mary, duuuuuh!!! (note the use of exclamation marks).

    Re: EffectMeasure — Flu in Vietnam — and wherever you live (Posted on: December 31, 2006 by revere).

    It appears that during 2006, in North America (guess this includes Canada), the main circulating flu typed A virus has been an H1 rather than H3. So, I intend to alter my shortstory draft “Eat The Meat” to mirror this CDC weekly flu report-based fact.

    Yes, on the subject of PCR testing (your post) — GM genetic modification has 90+ percent probably created H5N1, so don’t even bother reading the following info and links from two years ago on how PCR (same method used to check for HIV infection) can be used to find out other interesting scientific thingy-thangs…

    Cheers:*) and Aloha pumehana — Jon

    Date: Wed, 5 Jan 2005 18:40:41 -0800 (PST)
    From: “jon singleton” Subject: FaithfulAmerica: The U.S. Senate has a “Tortuous” Decision To Make [GM Foods Consumed by Millions *H5N1 Update* Version]

    C21*S*E*Research — GM Foods Consumed by Millions…

    “Dammerung”– that relentlessly hypnotic late 90s toon
    by Frontside, has been an inspirational (via shuffle
    repeat) “task master” in my engagement with this
    brief passage from ISIS Press Release 22/12/04 — US
    to Rubber Stamp Transgene Contamination…


    Excerpt: “It is already virtually impossible to test
    for the presence of experimental GM food crops in
    foods imported from or processed in the US, because
    over two-thirds of US field trials of experimental GM
    crops involve one or more genes classified as
    confidential which therefore cannot be detected.”

    (((C21*S*E*Research Note)))

    So, I’m wonderin’ if the same or similar PCR testing
    conducted by Chapela and Quist [data published in
    NATURE back in 2001 — see ISIS article “Who’s Afraid
    of HGT” and this article from CropChoice.com’s editor Robert Schubert, “Nature disavowal of article aside, transgenic corn contamination in Mexico still likely” @ http://www.cropchoice.com/leadstrye12a.html?recid=639), could be a possible detection avenue?!

    Find evidence of the CaMV 35S promoter in any given GM
    crop/processed food batch test sample, and see what
    sorta gogo funky sequence fluidity is remix happening
    around this gene switch “used in all transgenic crops
    commercialised” (see below) !?!

    ISIS Press Release 06/03/02 — Who’s Afraid of
    Horizontal Gene Transfer?


    Excerpt: [Using inverse PCR] Chapela and Quist were
    specifically looking for sequences linked to the CaMV
    35S promoter, and they found a diversity of them, many
    not linked to other parts of the transgenic DNA in
    transgenic maize…

    Four of the six samples (cobs) tested positive for the
    CaMV 35S promoter used in all transgenic crops
    commercialised… Sequence analysis at the site of
    transgene insertion by inverse PCR yielded 1 to 4 DNA
    fragments differing in size in each sample. The
    sequences downstream of the CaMV 35S promoter were
    diverse [sequence fluidity has done its thang and HGT
    remix-expressed around this gene switch]…

    This observation is consistent with our warning that
    CaMV 35S promoter has a recombination hotspot, and is
    hence expected to enhance horizontal gene transfer and

  5. #5 maryinhawaii
    January 1, 2007

    Jon, what I wrote to you was that every time I open your attachments they never open, I just get a page of addresses. What I asked you was “do you CHECK that LINK of yours yourself?” I did not ask if you checked sources, information, etc. I was trying to let you know that you are sending people information that they can NEVER OPEN!
    I also mentioned that I had written you previously about this problem, but gotten no response and no change in the problem, so I don’t think you read email responses to your posts.

    Frankly, I am getting annoyed with your personal attacks (this is numero two) You presume I, as well as everyone of “baby boomer” age is a homophobe because your parents were. Sorry if your parents were, but that doesn’t mean the rest of us are.

    My beloved sister, who died two years ago from breast cancer, was a lesbian her entire adult life. So what? That’s the least important thing to say or worry about a person. What she was was a highly esteemed Justice in the Supreme Court of Victoria, BC. What she is, is missed.

  6. #6 M. Randolph Kruger
    January 1, 2007

    Well I for sure am not a homophobe.I am scared of their blood though in combat situations or it entering the nations blood supply. Even today it still makes it in. So for me to Jon, just say no at the blood drives . Else lets go get a drink and I’ll even let you take the name of Reagan in vain. Sorry about your sis MIH. I am sure she went out of her way to be “even”.

  7. #7 ZoKun
    January 2, 2007

    Returning to the original focus of this discussion, it is worth noting that the H1N1 virus currently in circulation among human populations worldwide is a lineal descendant of the deadly, avian-derived “Spanish Flu” virus of 1918.

  8. #8 Wayne
    January 2, 2007

    The information you revealed today was interesting.

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