Repost (mostly): An Influenza primer

This is largely a repost from last year, but it turns out we have some readers new to this site who are interested in knowing some of the basics, so here goes.

There are three major sub-types of influenza virus. B and C don't cause big problems but type A is a major drag on the human condition -- in part because it's also a bummer for pigs, horses, Flipper and Shamu, and birds, which means we can't get rid of it. Influenza A replicates sloppily, which means it is constantly mutating. These small mutations are why the flu shot you got last year won't work this year. But the even worse part is that the virus can swap whole gene segments.

That's bad because the virus has a protein called haemaglutinin (HA) that sticks out from its surface and gets it into cells. There are 15 known major sub-types of HA, in virus that infects birds, but only 3 sub-types are known to have been prevalent in the human population -- called H1, H2, and H3. So, if a variety with, say, H5 were to develop the ability to infect humans, we'd be up a very thick and sticky creek, because nobody on earth has any immunity to H5 influenza.

Starting in 1997, there have been recurrent outbreaks of an H5 strain (specifically H5N1, with the N designating another protein called neuraminidase, which is less important to infectivity) in domestic and wild birds in Asia, which in at least two countries, Vietnam and Thailand, have infected people. (Note: Since I wrote this, of course, there have been human cases in China, Turkey, Iraq and Indonesia, as well.) This strain causes very severe disease and has killed young and healthy victims. It has also shown (so far) limited ability to be transmitted from person to person. H5N1 is now firmly entrenched in Asian bird populations and it's showing up in all sorts of unexpected places -- even tigers, which is really novel. Many experts believe it is likely only a matter of time before an H5N1 strain hits on the right combination of mutations to become highly infectious among Homo sapiens, and then, Kapow! -- by which I mean millions of seriously ill Americans (not to mention the rest of the world), severe disruptions to international commerce, an overwhelmed health care system, and, if enough people are sick at once, possible break downs in public services causing all sorts of collateral damage.

(To clarify, which I probably did insufficiently the first time, the idea is that the basic structure of the H5 haemagluttinin spike remains the same, but the virus undergoes other, small mutations that enable it to pass efficiently from human to human. This can happen either by random mutation, or by genetic recombination with other viral strains in dually infected humans or even swine.)

Other bloggers are on the case regularly, so that's all I'm going to have to say about this for now. Except that, in conclusion, our wartime President has diverted vast quantities of public health funding and planning to the threat of bioterrorism, which has now become largely synonymous with public health emergency preparedness. This has meant not only immediate misdirection of government resources, but also a cultural blind spot. Nature is still out there folks.

And, as a further update, since I wrote this our wartime President finally noticed the problem. The response, however, has been inadequate and largely inappropriate. I commend interested people to the Effect Measure blog, where this is covered very closely by a real expert, which I'm not. The last really major flu pandemic, in 1918-19, was also an avian flu. It decimated troops fighting WWI, and probably contributed to the end of that conflict. Lesser pandemics have happened since.

Further addendum: I realize that I also need to explain that, while ordinary seasonal flu and pneumonia mostly kill frail elderly and immunocompromised people, past pandemic flu strains, and H5N1 so far, have preferentially killed young and healthy people. The reason seems to be that the killing mechanism is a hyperactive immune response, a so-called "cytokine storm" (cytokines are molecules that cells use to signal each other, which are essential to immune response) in the lungs, that causes the lungs to fill with pus and fluid so that the victim drowns. Younger people, with more active immune systems, are actually more at risk than us semi-codgers. The only way to keep people alive through this is with mechanical ventilation, but there aren't nearly enough ventilators to go around. Sorry for the major bummer folks, but y'all need to know. This may or may not happen, but it's a legitimate concern. Probably fewer than 5% of sufferers will actually die, but that's still potentially a lot of people. And 30% of the population or so will become ill, if the event is like 1918.