The Ever-Surprising Swine Flu

Last March a new kind of flu came on the scene–the 2009 H1N1 flu, a k a swine flu. Hatched from an eldritch mingling of viruses infecting humans, birds, and pigs, it swept across the world. Here in the United States, the CDC estimates that between 41 and 84 million people came down with swine flu between April and January. Of those infected, between 8,330 and 17,160 are estimated to have died. For more details on the evolution of this new flu strain, here’s a video of a lecture I gave in November.

This flu strain has been nothing if not surprising. It was lurking around in humans for several months, undetected, before becoming a planetary infection. And before that, the ancestor of the virus was circulating among pigs for a decade, again unknown. And while the new swine flu has killed some 10,000 people in the United States alone and many more abroad, it has proven to be relatively low key–as flu goes. Some 30,000 people die in the United States every year from seasonal flu, the cocktail of flu strains that show up year in and year out.

Now the swine flu is surprising us once more. It has dwindled away to very low levels and stayed there. Meanwhile, the seasonal flu, which was expected to kick in at some point as well this flu season, is a virtual no-show. The San Francisco Chronicle has the story. In this CDC chart of total reports of flu-like symptoms, you can see that we’re in a deep trough. At this point in previous years, we were fast approaching the peak of the flu. This season, the peak came months ago, at the height of the fall swine flu outbreak.

When swine flu started to crash, some observers expected it to bounce back soon, as other flu strains have in the past. Ian York, at his blog Mystery Rays from Outer Space, offers some interesting ideas about why this hasn’t happened. He suggests that the virus has been stymied by pre-existing immunity in a lot of old people, new immunity from vaccinated children, and the protection that infected survivors now have. In other words, the virus just doesn’t have enough hosts now to sustain a new outbreak.

It’s possible that the swine flu’s raging success in the fall may have also led to the weird situation we’re in right now, with no seasonal flu at exactly the time you’d expect it. One possibility is that getting sick with swine flu provides some cross-immunity to seasonal flu. Another is ecological: the swine flu outcompeted seasonal flu so effectively at the start of flu season that the seasonal flu hasn’t been able to get a toehold since.

That, of course, could change. Seasonal flu has been known to peak as late as March. And while flu may be in a lull in the United States, it’s doing just fine in other parts of the world. For example, a nasty kind of flu called influenza B is raging around China right now according to the Chronicle. In normal years B makes up a pretty small fraction of US flu. But this is no normal year.

Scientists did a better job tracking the 2009 H1N1 outbreak than they have with previous emergent strains. They’ve got new machines to sequence virus genes, online databases to pool information from around the globe, and powerful computers to help figure out where the viruses came from. And yet, with just ten genes, the flu still continues to move enigmatically ahead of our understanding.

0 thoughts on “The Ever-Surprising Swine Flu

  1. Two friends came down with the flu this weekend. Anecdotes do not good science make, but I would not be surprised if it was a late peak this year.

  2. I wonder, also, if the level of people who got immunized for seasonal flu was significantly higher this year than in past years, thus creating a similar scenario for season flu. I know, anecdotally, that more of my friends and colleagues got seasonal flu shots during the period when anxiety was high and the H1N1 shot was unavailable. I don’t know, however, if that was true at a statistically valid level across the country.

  3. It would be interesting if turns out that the seasonal flu never does make a major impact in the US once the dust settles on flu season and that it turns out that it’s due to increased herd immunity due to increased vaccination rates and/or cross-immunity as you said. Like other commenters I also anectodally noticed what appeared to have been increased numbers of people coming out for flu shots this year but I haven’t seen any statistics on it yet.

  4. The latest Readers Digest has a nice short interview with Kathleen Sebelius, secretary of the Department of Health and Human Services. Nice article.

  5. The cross-reactive thing is really interesting. It’s been a vaguely consistent observation that new pandemic influenzas oust the previously-circulating seasonal strains. (Happened in the 1957 and the 1968 (but not 1976, which was actually a reecurrence of a previously-circulating flu). As far as I know, the reasons for this replacement of viruses isn’t really known. It’s hard to imagine any cause other than adaptive immunity. The ecological argument (“the swine flu outcompeted seasonal flu so effectively at the start of flu season that the seasonal flu hasn’t been able to get a toehold since”) doesn’t have any mechanism that I can see other than immunity.

    But the whole point about pandemic strains is that they don’t cross-react immunologically with previous seasonal strains, so there’s a large non-immune population for them. Study after study has shown that there’s no cross-immunity between previous seasonal strains and the new H1n1, so how could immunity to H1N1 cross-protect against seasonal strains?

    The most obvious explanation is that the studies measure antibody-based immunity, not T cell-based immunity. T cells are expected to cross-react much more widely than antibodies. But then why don’t we get T cell-based immunity every year?

    Perhaps the cross-reactive T cell immunity is short-lived enough that a previous season’s immunity doesn’t carry over for a year, but immunity from fall H1N1 still protects against winter H3N2. I’m still not very comfortable about this argument — it seems just too fine-tuned, for one thing — but I don’t see other simple explanations.

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