A Break From Swine Flu Panic

April 30th, 2009 by Clint

Believe it or not, there is good news to be found on the 2009 swine flu outbreak. This post is a compilation of the news that’s been the most reassuring to me, and contains no bad news or further panicking. Really.

The first and best bit of good news is that many people now know the best ways to keep from catching the flu. Wash your hands often, keep your hands away from your face, and avoid contact with the ill. If we adopt this as a way of life, and not just as a panic response, we’ll see a dramatic fall in cold and flu infections at large.

The next piece of good news is that we haven’t seen a revision of casualty estimates to include recent hospital cases. This is an indication that we’re still in the early stages of the outbreak, which gives us the most leverage for intervention. And so far, as more cases of infection are being discovered, we’re not seeing a corresponding increase in fatalities that matches previous pandemics.

Have I mentioned that I work with some great people? The day before the media picked up on the Flu outbreak, my co-workers had a paper published in BMC Microbiology on work they did last year: “Conserved amino acid markers from past influenza pandemic strains”. Surprisingly relevant, huh?

[Update: An article in Wired, Swine Flu Genes Show Virus May Be Weak, published on May 5, featuring my boss and my co-worker, although the science has been sensationalized a bit.]

[Update: A news broadcast, Computers decipher H1N1 genetic secrets, that aired on June 14 featuring my co-workers. I also make an appearance in the video, sitting at a meeting.]

Which brings us to even more good news: based on the data in Jonathan’s paper, the circulating strain exhibits only a fraction of the markers associated with the worst pandemic strains. While there’s always a causation versus correlation concern, if the markers prove reliable, this may mean the current strain isn’t a worst-case reassortment. As an interesting aside, both the markers and the genome sequencing seem to indicate that the strain is primarily a swine strain with some avian characteristics.

To round things off, you can’t catch the flu by eating pork, and there are still multiple anti-virals that are considered effective at treating the circulating strain.

I hope the good news will keep rolling in, and that we’ll be able to look back at this as a modern model for handling outbreaks.

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The 2009 Swine Flu Outbreak: This Is Not A Test

April 26th, 2009 by Clint

My thoughts are with the victims of the Flu outbreak in the U.S. and Mexico. This is a historic event, and we can expect the news to stay saturated with coverage reminiscent of the SARS outbreak of 2003. This morning in Mexico City, 20 are confirmed dead from the Flu, mass gatherings have been suspended, and schools will remain closed until at least May 6.

You can avoid infection by avoiding close contact with the sick, by cleaning your hands often with soap and water, and by keeping your hands away from your eyes, nose, and mouth. If you are sick, you must stay at home, which you should be in the habit of doing anyway.

There is some good news. The outbreak was discovered much sooner than I expected we could, and that will save lives. To help show how this saves lives, below is a generic epidemic curve.


Disease spreads from person to person up to a peak, and then tapers off as potential hosts are exhausted from the population. Underneath the curve is a second curve, showing deaths caused by infections. The reason I work on disease detection is to try and make these curves as small as possible. The earlier you intervene in an outbreak with treatment and quarantine, the smaller the curves will be.


This Flu strain is H1N1, and in case you’re wondering, there IS significance to the 1’s. This is THE Flu. H1N1 is the type of the 1918 Flu that raged across the world, killed more than twice as many people as World War I in a tiny fraction of the time, and for some reason disappeared from our collective memory. For the “normal” flu that we see every single year, the mortality rate is about 0.1% (1 person dies for every 1,000 infected). A low estimate of the 1918 Flu mortality rate was 2% (200 people died for every 1,000 infected).

Part of the reason so many die from this strain is that one of the most magnificent things in our corner of the universe, the vertebrate immune system, becomes perfectly useless by overreacting so badly that it kills us. Healthy young adults make up the majority of deaths because they have very strong immune systems which can’t stop fighting.

Flu Shy, Don’t Bother Me

There is hope that we can strike down this outbreak like we did SARS. If we succeed, then there’s a chance we’re not too far from finally stopping the “normal” Flu, which every year kills 30,000 people just in the U.S. That’s ten times as many people as perished on September 11, and 75% of the yearly car accident fatalities.

I’ve been telling people I want to make a Flu movie. I imagined it as narrative fiction, and desperately don’t want the opportunity to make it a documentary. We can tell some great stories about love and life centered on the Flu. We don’t need the ridiculous fictitious diseases that haunt theaters. I’m horrified that we accept the Flu as a normal thing, and the coming of it as uncontrollable as Fall or Winter. I hope it goes the fuck away.

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