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.