How it works
"Your immune system (when it’s working right) recognizes self and non-self. It protects the self and attacks the non-self. It does this in a couple of ways. First, you have generalized reaction. When cells are distressed, they release cytokines, and those switch on a kind of white cell called the NK-cell. NK stands for Natural Killer (no, I’m not making this up). The NK cells find anything they don’t recognize, and, using specialized proteins, destroy it. When you’ve got an infection, those are the first things that come on line.

The next thing to arrive are the antibodies. These are specialized cells that are keyed to find one specific protein—the foreign invader protein—and destroy it. Before your body can produce antibodies, it has to have been exposed to the antigens (which is what you call non-self proteins), and be sensitized.

Meanwhile, your body is releasing enzymes, hormones, peptides, and other chemicals that act as messengers to produce various effects. Fevers, swelling, sweating, headache … all enzymes. The aching in your bones that you feel is the marrow pumping out white cells to fight the infection.

Once your body has successfully fought off an invader, the antibodies remain. If they ever again encounter proteins of the same shape, they’ll be on ‘em fast. The infection won’t have a chance to start.

Now, your influenza virus is a simple one. It doesn’t even have DNA in it. It has strands of RNA in its center. RNA mutates pretty fast. But here’s the really tricky part about the flu: it has a sneaky way of getting past the immune system, even if you’ve had the flu before. The shell or capsule that surrounds that RNA is made of two proteins, hemagglutinin and neuramidinase. Hemagglutinin and neuramidinase can move like the tiles in a sliding-block puzzle, presenting different protein shapes to your antibodies. Hemagglutinin and neuramidinase are the H and N that you see when people talk about Influenza H5N1 or H1N1 or H3N2 or what-may-have-you. There are fifteen known types of hemagglutinin and nine known types of neuramidinase, and they have subtypes below that. Those two substances keep moving around, so that antibodies don’t recognize them. This is called “antigen drift.”

It only gets better after this.

Viruses have the ability to pick up useful traits not just by means of mutation, but by grabbing them from other microbes directly—even across species lines. Flu, moreover, doesn’t have a single strand of RNA inside it—it has unconnected strands. So if two viruses infect the same cell at the same time, the RNA can play mix-n-match, take virulence from one virus and infectivity from another, and come up with something both infective and virulent. (That’s what happens when a swine flu or an avian flu gets loose: Someone has both human influenza and swine or bird influenza at the same time, the two viruses enter the same cell at the same time, and what comes out shares the worst features of both.)

As I keep saying, flu is as simple as drool. It only has eight genes in its genome. Those genes insert themselves into the living cell’s genes, and start producing viruses. In about ten hours, the infected cell explodes and releases somewhere between 100,000 and one million brand-new viruses into the body; and, through coughing and sneezing, into the world. RNA doesn’t have a checksum. And when you have unconnected strands of RNA, you have a high probability of mutation. So all of those million new viruses won’t be exact copies of the original. We’re seeing mutation on steroids, figuratively speaking. Pretty much every possible combination will be present. That means that influenza strains can adapt rapidly to different drugs, to different environments, to different species.

Other RNA viruses include measles and HIV. They’re both nasty. But HIV is very hard to catch, and measles never changes its protein shape so having once had it (or vaccination) lends permanent immunity.

Once influenza starts cooking, you have a lot of virus in your body. And this is where the swine flu gets not just miserable but rapidly lethal. Remember those cytokines, the chemicals released by cells-in-trouble that cry havoc and let loose the Natural Killer cells? Get enough cytokines going, and you’ve got two kinds of trouble. First, those NK white cells they activate are fairly large. In order for them to get to the scene of the infection, the capillaries have to be weakened so that the NK cells can pass through their walls. This also allows fluids to pass through. Your body starts dumping fluids through the capillaries and into your lungs. The ultimate effect is viral pneumonia. If it’s bad enough, you drown. "

Copied from a Making Light post that's chock full of useful references for people worried about swine flu.
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