A quick look at the H1N1 data

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I'd been mostly avoiding developing an opinion on the H1N1 pandemic, but I recently had someone ask me about it and then watched this ABC reportCogitamus) and figured it might be time to read some of the literature. Your go-to site here for statistics is CDC FluView (the above report complains about availability, but I don't think anyone is claiming that CDC is actually misreporting the data). After reading through CDC's data, the situation seems to be as follows:
  • We're seeing over twice as much "influenza-like illness" (ILI) as normal this year (5.5% of visits versus 2.3% of visits).
  • When tested, the majority of these cases (70+%) aren't actually flu.
  • The vast majority of cases that are actually flu are H1N1.
  • Mortality from pneumonia and influenza is currently at 7.5%, what looks like about 50-75% over the seasonal baseline and over the 6.9% epidemic threshold. So, you're looking at like a 2.5% excess risk of death. This doesn't sound too bad for adults.
  • We're seeing something like 2x ordinary pediatric mortality: 20 deaths in the week Nov 7-14, 138 deaths since August 30 and 200 since April 30. It's difficult to compare here since the CDCs ordinarily mortality data is broken up into different cohorts. Ordinarily there are around 10,000 deaths in the US in 2006 in the 1-14 cohort and 35,000 in the 15-24 cohort [*]. It we crudely divide by 52, we get something like 200 deaths/week in the 1-14 cohort and maybe something like 400 deaths/week in the the 1-17 cohort (assuming its evenly distributed in the 15-24 range). So, this year's flu represents somewhere around 2-10% excess mortality over usual, which doesn't sound that bad.
  • It looks like the rate of flu is coming down both in the US and Canada. The Canadians say they may have reached their "epidemic peak".
  • Quebec appears to be plague central, with the highest rate of hospitalizations of any province in Canada.

I'm most struck by how high a fraction of people with disease suspicious enough to be tested actually turn out not to have flu. This isn't just a case of US health care overtreatment, either, The Canadian positive rate is a little over 40%. That said, the rate of positives varies really dramatically from region to region, with a low of 13.3% in region 6 (AR, LA, NM, OK, TX) and a high of 51.8 in Region 3 (DE, DC, MD, PA, VA, WV), but it's hard to tell (or rather I'm too lazy to run the numbers) if it's just a matter of basic incidence or of the amount of testing being done.

One question people seem to want to ask is: should I get the vaccine? I know there are concerns about side effects, though as far as I can tell, there isn't much to be worried about (you can find the CDC party line here and Wikipedia's rundown here): the US versions of the H1N1 vaccine seem to be made with the same methods as the seasonal vaccine, so if you were happy to get that, you should be OK with the H1N1 vaccine too. [There have been concerns about the vaccines used outside the US which contain adjuvants, and I haven't developed an opinion on that.].

As far as effectiveness goes, the studies that are available seem to use the stimulation of an immune response rather than actually getting H1N1 as a study endpoint. This is understandable, since randomized controlled trials with infection as the endpoint are slower and more expensive to do, but it makes the data less useful for decision making than it otherwise would be. This Atlantic article argues that the overall evidence for flu effectiveness is thin, but compare this CDC survey which seems to indicate effectiveness in the 55-85% range. Anyway, if we assume that your chance of getting the flu is 5-20% and everyone gets vaccinated, then we'll see something like a 3.5-15% reduction in disease cases (number to treat = 6-30). On the other hand, since apparently most cases of ILu aren't actually flu, the improvement in your chance of experiencing some sort of flu-like crud (which is after all what you care about) are only like 1-5%, ignoring, of course, that flu season seems to be mostly over now.


There are two motivations for getting the vaccine: to prevent flu in yourself, and to prevent you from spreading it to others if you are infected. The latter can be much greater than the former. If I got H1N1 and was really sick for a week, I would be bummed but resigned to it. If I got H1N1 and passed it on to a more susceptible person who then died, I would probably have a much harder time forgiving myself. This is my logic for getting the vaccine after they open it up to non-threatened populations. I have never gotten a normal seasonal flu shot, and probably won't start for another 15 years, but the deadliness of H1N1 has me more concerned for my possibility for passing it along.

One of the more concerning things about H1N1 has always been that it's killing a significant number of people who do not have suppressed immune systems, so it's not really sound to assess your own risk as a function of your age and general health. Health Canada recently estimated a third of confirmed H1N1 deaths in Canada fit this category.

Paul Hoffman's point about preventing spread is correct, and is a flaw in EKR's calculations. If a high enough percentage of the population gets immunized, infection rate will fall to zero, because 'herd immunity' is achieved where there aren't enough vulnerable people for the virus to sustain its spread. Because of 'network effects', the number of reduced flu cases due to a single administered dose of vaccine is greater than the vaccine's efficacy for that individual.

This is also the theory behind some governments promoting universal seasonal flu vaccination (the Ontario government has been doing this since 2000). I receive a seasonal flu shot every year because it is conveniently offered at my workplace and takes 10 minutes out of my day. Not only am I reducing my own chance of getting the flu that year, but I am also protecting other people who are at higher risk of severe complications. There are also some ancillary benefits to universal vaccination such as fewer lost work days due to illness and (surprisingly or not) a significant drop in use of antibiotic.

The safety of the vaccine is pretty good. Your chance of having a serious reaction -- particularly if you have not had a reaction before -- is very low.

The effectiveness is another issue. That Atlantic article has been torn to shreds on places like scienceblogs and sciencebasedmedicine. Although the one point that really stuck is that we didn't see any noticeable decrease in mortality in the years that the flu didn't take, and I haven't seen any of the people who fight the antivax dummies address that point.

The effectiveness of flu vaccines is pretty clearly demonstrated in labs. I don't know if it does or doesn't work in the real world; it would not be unheard-of for something to work amazing in a clinical setting but totally fail when tried on the general public.

Like Paul Hoffman said, I don't want to be a vector. Given the low risks, I still get seasonal flu shots, and will probably get H1N1 at some point (I'm not in a high risk group and am giving them time to "go first," but I don't know how long that will go on). My kids are either done with their H1N1 shots or in the process of getting them.

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