Effect Measure

Flu season

Everyone knows it’s flu season. We see the evidence in birds and people with H5N1. The Indian subcontinent is awash in birds with H5N1. Sometimes here we forget to remind people it is also flu season with the regular circulating subtypes, H1 and H3 and this is shaping up to be a predominantly H1 season in Europe and the US.

In the US:

During week 3 (January 13 – 19, 2008), influenza activity continued to increase in the United States.

Three hundred twenty-nine (11.1%) specimens tested by U.S. World Health Organization (WHO) and National Respiratory and Enteric Virus Surveillance System (NREVSS) collaborating laboratories were positive for influenza.

The proportion of deaths attributed to pneumonia and influenza was slightly above the epidemic threshold.

The proportion of outpatient visits for influenza-like illness (ILI) was above national baseline levels, and the proportion of outpatient visits for acute respiratory illness (ARI) was below national baseline levels. The East North Central, East South Central, Mountain, New England, Pacific, West North Central, and West South Central regions reported ILI at or above their region-specific baselines.

Six states reported widespread influenza activity; 17 states reported regional influenza activity; 17 states and the District of Columbia reported local influenza activity; 10 states and Puerto Rico reported sporadic influenza activity. (CDC Flu Surveillance site)

Here is how things have shaped up so far this season:


It’s flu season in Europe, too. Most isolates are also H1:

Increased influenza activity was reported in 13 European countries in week 2 of 2008: Austria, Bulgaria, France, Hungary, Ireland, Italy, Luxembourg, the Netherlands, Portugal, Slovenia, Spain, Switzerland and the UK. Based on historical trends, influenza activity is expected to increase in more countries in the coming weeks and to move gradually eastwards and northwards in Europe [1]. Influenza activity is mainly associated with type A influenza virus, subtype H1, which usually causes only mild- to medium-intensity influenza epidemics. (Eurosurveillance)

It’s clear flu season is well underway. We can expect it to go full tilt at least through March. The same thing will be happening in those areas where H5N1 is endemic in poultry and where sporadic cases of human H5N1 occur. This is something to keep in mind when there are reports of dozens, sometimes hundreds of “suspect” cases appearing in an area where there are one or more H5N1 cases. Those “suspect” cases are happening right now, without any H5N1 anywhere near them. It’s just that no one is paying any attention because it’s flu season.

The good news for seasonal flu is that H1 seasons tend to be less severe in terms of excess mortality than H3 seasons and the predominant strain of H1N1 circulating this year is included in the flu vaccine.

I got a flu vaccination again this year. There remains some controversy about its effectiveness in my age group (65+) but I’m hoping for some antigenic effect. If you are younger than me (and, alas, most people seem to be these days) I’d definitely advise getting a flu shot. It’s not too late and you don’t want to get the flu. Maybe H1N1 or H3N2 aren’t H5N1 but they are bad enough. If you’ve had genuine flu you already know that. If you haven’t, well, I hope you don’t get it.

If it doesn’t kill you it won’t make you stronger, either. Trust me.


  1. #1 herman
    January 28, 2008

    Could the spread of H1N1 and H3N2 in Indonesia facilitate the transmission of H5N1 to humans? Also, there may be other vectors than birds for H5N1.
    Please note reports from Indonesia regarding human H5N1 infection specify a 9 year old boy who tested positive, died on Monday. That is death 99.
    A 31 year old woman and a 32 year old man are in Persahabatan hospital. They both have serious breathing problems and also tested positive.
    A 23 year old woman died on Sunday with suspected bird flu, and genetic test results will be reported soon.
    Do you remember when the reports from Indonesia indicated perhaps one, or at most 2 people infected with H5N1 in a week or 2 weeks?
    Now they are reporting 3 or 4 people either dead or infected in a week or less.

  2. #2 revere
    January 28, 2008

    herman: One could argue that the co-circulation of other subtypes could promote a reassortment or recombination of unknown properties or that cross reactivity of the N1 would inhibit an H5N1. NB: birds are not a vector. They are a reservoir. And, yes, people here keep track of what goes on in Indon even if we don’t mention it every day. Coals to Newcastle.

  3. #3 speedwell
    January 28, 2008

    Revere-author-of-this-post, I heard something recently about the flu shot only being “good” for several months, making the end of flu season a vulnerable time even for those who got vaccinated on time. I think the idea was that the vaccine lost its effectiveness in the body after a period of time, which doesn’t sound right. Maybe the way it works (if it works) is that the flu virus mutates out of the scope of the vaccine within several months. What is the science on this?

  4. #4 M.Randolph Kruger
    January 28, 2008

    Revere-Specifically what is “Unsubtyped”? Is it they cannot identify it or is it a new strain of H1 or H3?

    Speedy-Antigenic shift, drift, mutation… pick a term. The flu vax is a “best guess” each year for the strain by main type that might be sexed up a bit with something they know is out there. So by the time April rolls around its taken a mutation trip to someplace else. If you are lucky, it is close enough to do some good. Two or three years ago they missed the strain entirely. The results were obvious.

    Revere can expand on that a bit, but thats the general idea. A simple little shaping difference if you could see it is all that it takes to make it worthless, or worth something.

  5. #5 J-Dog
    January 28, 2008

    I just called my Primary Care Provider. The nurse told me that flu season is over. I suggested that it went through at least March, and she said no, it doesn’t and they are out of flu shots anyway.

    Is it time to shop for a new Primary Care Provider?

  6. #6 revere
    January 28, 2008

    J-Dog: Well, you might not want to depend on them for this kind of stuff. It depends on other factors. Life is a trade-off. But on this one, she is quite wrong.

    Randy: Un-subtyped means they didn’t determine (as in didn’t test for) what subtype of flu/A it was or it couldn’t be subtyped for technical reasons. It doesn’t mean it’s new subtype or not H1 or H3. Regarding the “guess” you note, you are right, although it is based on good data from the previous year’s circulating strains. As I understand it they guessed right on H1 this year but not H3. Mismatches occur every so often, although there is probably a good deal of cross-reactivity even between mismatched strains. The guesses are based on the surveillance system that is shaking because of Indon’s concerns. That system is mainly used for seasonal flu, not bird flu, and it is what produces the vaccine seeds for the following year.

  7. #7 carl
    January 28, 2008

    Looking at the ongoing reports from West Bengal and Bangladesh it is apparent that BtoB is quite out of control right now. I am defining ‘out of control’ in terms of an inability, at a practical level, of the Indian / Bangladesh governments to control the spread of the virus via culling. That situation is apparently the consequence of poor government management, lack of infrastructure, local social circumstances (poverty etc.). The question then becomes what is the consequence of that ‘out of control’ scenario? Presumably the level of infection declines when the birds (other susceptible creatures) are generally dead or depopulated to extent that contagion spread is minimized. Are more varients or sub-clades of virus spawned due to massive numbers of infections? Are any of those varients more dangerous to human beings and / or more transmissible to human beings (the situation in Indonesia appear to be due either to increased transmissibility BtoH or increased entrenchment of the virus in the local environment). presumably there will be a significant (perhaps massive as in a couple of thousand cases reported or not) number of BtoH infections in West Bengal / Bangladesh due to lack of precautions. That would be less a result of transmissibility than a result of thousands of unburied H5N1 positive dead birds laying around (if local media reports are accurate). It would however create a more significant chance of a more transmissible varient developing. It looks to me as if the events on the Indian subcontinent are significant in a way that Egypt and some other areas were not. We have not seen a situation where the situation is both out of control and there is a significant die off in the face of control efforts.

  8. #8 Shannon
    January 28, 2008

    Cart, you forgot to mention there is a strong suspicion that on some variants there is Tamiflu resistance. If that happens to be the case in West Bengal and Bangladesh…..

  9. #9 Helblindi
    January 28, 2008

    Well, I think I have read today a press release stating that even our own H1 has become at least partially resistant to oseltamvir. Too fast for my liking but that’s the way it is.

  10. #10 Racter
    January 28, 2008

    The “unsubtyped” thing is something I’ve been wondering about for some time, and while I appreciate the answer you just gave in response to Randy’s question, I still hunger for a little more detail. Every week when I check the CDC update, I look at that chart, and the bulk of the isolates are always in this category. I often wonder: so what’s the holdup with that, exactly? Is there an unspoken “yet” at the end of that? Is it considered safe to assume that the distribution in the isolates that have been subtyped is fairly representative of those that have not?

    I’m also curious about what it is that distinguishes one subtype from another, and what methods are used in making the distinction. I assume it has to do with structural differences in the glycoprotein, but despite having slogged through tons of abstruse online literature and looking at ribbon diagrams and so forth, I never have found any specific references as to just what kind of differences we’re talking about.

    Though I’m not a frequent poster here, I visit daily (at least), and have especially valued some of the more technical contributions you’ve made. If you can’t clear any of this up, I sure don’t know who can.

  11. #11 gilmore
    January 28, 2008

    O.K., from the Stupid Question Dept:

    Would it make sense to get a second flu shot later in the season to reactivate the immune response???

  12. #12 revere
    January 28, 2008

    gilmore: Not at all a stupid question. That’s the principle of booster shots. On the other hand, we don’t know it would do you any good either. It may be that whatever protection the vaccine produces is maxed out the first time. Or maybe not (I’m sure you get tired of hearing me say that, but I don’t know what else to say and be honest). Of course as a matter of policy, this becomes a bit dicey as there isn’t enough vaccine now for one shot per person, much less two.

  13. #13 gilmore
    January 28, 2008

    Certainly understand that I shouldn’t hit the buffet line a second time if everyone else hasn’t got to the trough for their first feeding. I’d just never heard of any reasoning, positive or negative about a second shot. . .

    P.S. Never tire of you saying you “don’t know”. There is so much stuff you do know that it is actually nice to see you don’t really know EVERYTHING, even though we have come to beleive you sometimes do know all.

    THANKS again for your work in this great blog

  14. #14 bc
    January 29, 2008

    It’s interesting that this is the first week so far this season that the number of H1 and the H3 isolates have been roughly equal in number on the graph, compared to prior weeks this season. I’ve had a hunch that H3 might emerge to predominate in late season in upcoming months; it may be starting. But as CDC says, “It is too early in the influenza season to determine which influenza viruses will predominate.”

    There are lots of myths about influenza vaccine: that it only lasts a few months, so wait till December or get a second flu shot; or that it’s not effective in older people. For a summary of good information for the layperson, see http://www.cdc.gov/flu/about/qa/vaccineeffect.htm (unfortunately, because it’s for the general public, the sources of their statements aren’t footnoted.)

    However a quick summary: If your immune system is able to respond at all, your response will last throughout the flu season. You can get your flu vaccine as soon as they’re available, and there’s no reason to wait till December. Studies have NOT shown a benefit from a second shot in the same season. For folks Revere’s age, the vaccine may not completely prevent illness, but even in nursing home patients the vaccine is 50-60% effective in preventing hospitalization, and 80% effective in preventing death, so still well worth getting.

    (And, Revere, I don’t think you look a day over 60!)

  15. #15 revere
    January 29, 2008

    Racter: Sorry, didn’t see your question until just now. The types are influenza A, B and C. The subtypes are determined immunologically. There are 16 broad immunologic types of HA and 9 broad immunologic types of NA on the outside of influenza A viruses, hence the subtypes. The subtyping is now done by identifying genetic sequences characteristic of the different subtypes that correlate with the older method of using specific antisera. Each of the subtypes can have smaller variations and these are the strains.

  16. #16 M. Randolph Kruger
    February 1, 2008

    Well the crud is running around in Tennessee so bad that instead of giving an ambiguous snow day tommorow they are closing schools in about 9 counties due to flu. They get their funding by average daily attendance and its money thing with the state. Baby Boy came in today and said he and four others were all that were in class and three teachers got smoked while they were there. They had to leave.

    Revere, so the H1 they got but they didnt add anything to the vax for H3.? How much of that gooey crap they inject into the arm is actually active. Had they guessed both would it have been more or the same gooey crap with the active ingredients in with a carrier liquid.

  17. #17 revere
    February 1, 2008

    Randy: The H3 component of the current flu shot is slightly mismatched but it’s there and probably provides some protection. But so far, the circulating subtype is mainly H1, although that can change as the season progresses.

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