Biology: November 2009 Archives


November 29, 2009

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.