Effect Measure

Data from the Emerging Infections Program (EIP), one of the component parts of the CDC national influenza surveillance system, is showing that for some segments of its population the US did indeed experience a second flu season. The segment of particular concern are children between the ages of 5 to 17 years old, and to some extent adults between the ages of 18 and 49. The EIP counts only laboratory-confirmed hospitalizations in 60 counties located in 12 metropolitan areas in 10 states (if you are wondering, the 12 metro areas are San Francisco CA, Denver CO, New Haven CT, Atlanta GA, Baltimore MD, Minneapolis/St. Paul MN, Albuquerque NM, Las Cruces, NM, Albany NY, Rochester NY, Portland OR, and Nashville TN). Here’s the method:

Cases are identified by reviewing hospital laboratory and admission databases and infection control logs for children and adults with a documented positive influenza test (viral culture, direct/indirect fluorescent antibody assay (DFA/IFA), reverse transcription-polymerase chain reaction (RT-PCR), or a commercial rapid antigen test) conducted as a part of routine patient care. (CDC, Hospital Surveillance)

CDC posts the EIP data on its surveillance web page and the latest version shows different rates for different age groups. The rates are the number of lab confirmed hospitalizations for influenza per 10,000 population and the dotted lines in each of the age strata represents the average rate for flu seasons (October 1 to April 30) in 2005-06, 2006-07 and 2007-08. Normally the rate during the late spring and summer months, shown in the chart below, are close to zero and are nowhere near the flu season rates (the dotted line). But in every age group we see a rise in flu hospitalizations and in the 5 -17 year old group it has been at flu season rates and getting close to that in the 18 – 49 year old group:


Source and larger version here.

That’s one view, anyway. Here’s a different one. There’s another part of the surveillance system called the New Vaccine Surveillance Network (NVSN), also lab confirmed influenza hospitalization rates, but for children less than 5 tears old that live in three specific counties: Hamilton County OH, Davidson County TN, and Monroe County NY. If a child is admitted to one of the NSVN hospitals with fever or respiratory symptoms they are tested via PCR and viral culture and rates estimated based on the catchment areas of the hospitals. This is a different population that the top two panels in the chart above:


Comparing this year to the last three flu seasons suggests it is like the others except for last year, which was exceptionally bad. But note also that the rates estimated in the NVSN are 3 to 6 times higher than the comparable age groups in the EIP. Why the difference and which to believe? Other than the fact that there are different geographic populations involved, the EIP is a passive system that depends on after-the-fact record review of cases where there was enough suspicion of flu to get lab studies done as part of otherwise routine care. The NSVN is an active prospective system whereby any child with fever or respiratory symptoms is worked up for a diagnosis of flu. So there are major differences in these two systems which makes them difficult to compare with each other quantitatively. I’m not sure if the EIP ran through the spring and summer months of previous years, so the internal comparison there is with rates from the same system during the flu season. Given the heightened concern about swine flu there may be more diagnostic work-ups for flu this summer, too, so a comparison even if possible might not be that informative. The NVSN is a much more restricted system as far as geographic representation is concerned (3 counties). Given the very patchy nature of flu this is also a problem, but at least an internal comparison is possible and doesn’t suggest anything out of the ordinary — in these 3 counties. On the other hand, the EIP and general impressions are that the under 5 year old group is not the one hit hardest but the next age stratum, 5 – 17, which is not included in the NVSN. [NB: Marc points out in the comments (#10) that while both systems are cumulative rates they cumulate from different time points, which is yet another reason — and arguably the most important reason — why they differ. So while all I said remains true, I think I missed the most critical difference. As politicians sometime say, “Mistakes were made.” And this one was made by me. Thanks to Marc and apologies to readers.]

The influenza surveillance system is a patchwork of different parts and wasn’t designed to follow a pandemic. Indeed this is a circumstance which is historically unique in medical history, watching a pandemic unfold in real time. Surveillance, alas, is the poor step-child of public health and has never gotten its due share of resources or the intellectual respect it deserves. So meanwhile we’ll have to make the best of it and try to read the entrails.

And what I see is a second flu season for the 5 to 17 year olds. But I could be wrong.


  1. #1 Jude
    July 17, 2009

    My son’s summer camp was cancelled last week because 10 kids and 3 staff members came down with the flu. It hasn’t been confirmed yet if it was H1N1, but I felt a little panicky because he has asthma. Then reports came in that a large percentage of the freshman class at the Air Force Academy has confirmed H1N1. Both of these incidents are from Colorado. I’m thinking, wow, all this influenza in the summer–it seems odd.

  2. #2 Nanci
    July 17, 2009


    First let me say I’m so glad I stumbled upon this blog, it is invaluable in my role at work as pandemic coordinator! I wanted to ask your opinion on children with asthma being vaccinated with pneumovax? My daughter has has infrequent reactive airway disease but is heading to camp in 3 weeks. In our province 9 camps have been identiifed (hers included) as having an H1N1 outbreak. No plans to close at this point. Would it be in her best interest to get this additional protection? It is certainly not being discussed here in Ontario and I’m curious what you think.

  3. #3 revere
    July 17, 2009

    Nanci: I try not to give medical advice here because I think that’s best done with your doc or pediatrician who knows the patient and circumstances. However I did discuss pneumovax here and there are links in that may be helpful.

  4. #4 albatross
    July 17, 2009

    I verified that my kids had had the childrens’ vaccine, and got mine a couple weeks ago. (I asked my doctor if it made sense, and he thought it did.)

  5. #5 Nanci
    July 17, 2009


    Thank you for the link to the past post – very helpful. I’ll be photocopying it for my doctor. I’m only baffled why public health messaging isn’t stronger on this very easy step to take for vulnerable populations.

  6. #6 Snowy Owl
    July 17, 2009

    Here is an old and pertinent Lecture made by
    Richard Feyman on

    Probability and Uncertainty, Tiny and Waves.. or something else?

    From Microsoft Research – Messengers Series

    Project Tuva


  7. #7 Curious
    July 17, 2009

    Nanci: I just returned from my allergist, who was not reassuring about H1N1 in the least, neither was my GP, so I think that, personally, I’m seeing public health coming around a bit.

    Anyway, I have a few questions:

    1) Is it possible that the bad flu season LAST year (2008-09) was in part due to swine flu that went unnoticed? I’d read they thought it might have been circulating as early as August — could it have been here even earlier, or would testing have caught it?

    2) Why is swine flu so patchy? It’s obviously pretty transmissable — as we saw in NY, and it’s reached even very remote regions — so why doesn’t it spread once it reaches some communities?

    3) My allergist said that this upcoming year’s flu shot would be at least partially cross reactive with swine flu — protecting 30-40%. Does that seem accurate?

  8. #8 Nanci
    July 17, 2009


    I’m not the epidemiologist in this crowd so I’m not the one who can answer those very specific questions, I’m redirecting them to Revere (and signing off for a week’s vacation!).

  9. #9 hornblower
    July 17, 2009

    I’ll take a stab at Curious’ q’s:
    1). I don’t think so. It would have shown up as untypable on the virus surveillance & with a large # of them that would have made people sit up & take notice.
    2). Answer this question & win big prize! Seriously, I think this is a huge question which nobody understands. I’ve heard suggestions about relative humidity which sound like they might have something there but afaik it’s all very theoretical.
    3). I don’t think so. From Canada’s Fluwatch:
    “Antigenic characterization also indicates that these viruses are antigenically and genetically unrelated to seasonal influenza A (H1N1) viruses, which suggests that there is little or no protection to be expected from vaccination with seasonal influenza vaccine.”

  10. #10 Marc
    July 17, 2009


    If I read right, NVSN is cumulative from week 40 of last year, while EIP is cumulative from week 15 of this year. Hence the slopes should be comparable but not the absolute levels, no? And the slopes are pretty hard to estimate by eye, but appear to be greatest around week 25 for EIP — can’t tell on NVSN as it ends at week 25.

  11. #11 revere
    July 17, 2009

    Marc: Hmm. I think you might be right. That’s an error on my part, for sure. Thanks for catching that. I’ll stick in a note.

  12. #12 elephantman
    July 18, 2009

    The following data from the Royal College of General Practitioners’ research and surveillance center in Birmingham, England published provides a snapshot on the current situation in the United Kingdom, where it appears a full blown epidemic outbreak is currently underway
    (source article available at

    The RCGP data cited UK Guardian report says children and teens are the group most heavily impacted, which corresponds with data being reported from Mexico.

    Notably, however, Mexico data indicate that the age group with the highest absolute numbers of confirmed cases (10-19 year olds) also has the lowest number of recorded fatalities.

    The he RCGP data from England indicate that children aged between five and 14 are the most heavily affected age group, with a reported incidence rate of 160 per 100,000. The rate among under-fives is 114 per 100,000 and 89.4 among those aged 15-44.

    The rate of people diagnosed with influenza-like illness in the north of England increased more than 500% in a single week, from 6.6 per 100,000 of population during 29 June to 6 July, to 37.2 per 100,000 between 6 and 16 July.

    Rates of infection more than doubled in central England from 42.8 to 93.9 per 100,000 [over this period] but only rose slightly in the south of England from 72.1 to 74.9 per 100,000.

    Cases in London – said to be one of the worst affected swine flu “hotspot” – declined from about 180 to 140 per 100,000 [over the period between 6 July to 16 July]. Across England as a whole the incidence increased from 51.88 to 73.42 during that week, a rise of 42%.

  13. #13 downeast
    July 20, 2009

    Revere: quick question, if you circle back to old posts.

    Do cultures of previous lab tests (say February) still exist at labs or are they tossed? Just wondering if the Type A H1 positive tests from mid-winter in a given state CDC are re-tested for H1N1. Thanks.

  14. #14 revere
    July 20, 2009

    downeast: Routine tests are tossed, but there are many collections of sera done for various reasons that are used to go back to reconstruct things. Some of that has been done but probably more will happen. There just aren’t enough hands and hours in the day to do everything that needs doing. Some things that sound simple are extremely time consuming and expensive, even though simple in concept. Most epi studies are like that (that’s what I do for a living).

  15. #15 Kelly Dizor
    July 23, 2009

    I just got the flu a couple days ago. I went to the emergency room. They said I cannot take the h1n1 test because I am not 65 years or 5years and younger , because the state is not giving out that much kits. My doctors office said the same thing. I’m 39 years old and I have diabetes and high blood pressure. The thing they told me to watch for is pnuemonia. Then I can come in and take an x-ray. I am very concerned also because I live with my elderly in laws. My father in law just got a stroke.

  16. #16 Paul
    August 26, 2009

    Does the flu virus mutate as it passes from person to person? If so, how does the vaccine work against mutations?

  17. #17 revere
    August 27, 2009

    Paul: The virus is a sloppy (i.e., mistake-prone) copier of its own genetic information. That’s what a mutation is. Most of these mistakes mean the virus won’t replicate any more. Every time the virus in a host cell makes a copy of itself (which it does by the millions or billions) some or many have these copy errors. That includes within a patient. “In between” patients it doesn’t change (there is no mutation) but when it gets to a new host some of the many variations will be more fit than others and come to predominate. If there are mutations in the part of the virus that the vaccine is directed against (only one possible change of many that there could be), then whether the vaccine will continue to work depends on the nature of that change. Some of them won’t affect the vaccine, some will.