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Is it a viral vs. bacterial thing? Is there just more variety among types of flu than other diseases, so that this year's vaccines don't cover next year's flu?

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The flu virus changes rapidly so that the current vaccine doesn't work against the new strains.

The way vaccines work is that they teach our immune system what to look out for. The vaccine contains bits of the virus but in a form that can't cause a proper infection, the body learns what to look for and next time before the virus can really get going the immune system kills it off first.

In the case of flu, every year it looks different enough that the targeting mechanisms of our body don't recognise it. Flu being a RNA virus frequently mutates until it is slightly different. This is called antigenic drift, the changing of the antigens or the parts our body recognises.

On top of that there's lots and lots of types of the influenza virus, that can not only infect humans but others which affect other animals. Occasionally the virus might combine with a random other strain making it completely new: an animal flu and human flu hybrid. These are the epidemics of swine or avian flu etc. This recombination is called antigenic shift.

So each year scientists predict which viruses will affect us this coming year and grow them ready for vaccines. Of course there's some of the old virus floating around looking for someone to infect, but those infected can't be infected by it again if the immune system is working.

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Thank you! Looking based on your answer at the wikipedia page for RNA viruses I see that polio and measles are also RNA viruses. Why don't they mutate as quickly as the flu? Or is there just less biodiversity among those viruses than the flu? –  kuzzooroo Mar 11 at 2:05
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HPV is a DNA virus that mutates at the same rate as our DNA. In comparison, there's the viruses you mentioned that mutate slowly and HIV another RNA virus that mutates so fast every couple of copies has a mutation. RNA itself is less stable, so RNA viruses mutate. However the real mutation rate is all about the error checking of the enzyme. HIV has no error checking basically and doesn't care. Increased mutations means more variability and immune escape but more non-functional virus particles. Too much or too little is a bad thing. –  AndroidPenguin Mar 11 at 9:01
    
OK, I think I understand. The influenza virus does less error checking than some other RNA viruses and so it mutates faster. Is that right? –  kuzzooroo Mar 11 at 11:47
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Yup! The scientific term for this is that the polymerases lack proofreading. –  AndroidPenguin Mar 11 at 15:35
    
@kuzzooroo Hi ! If you think androidpenguin answered your question, please "accept" it as an answer by clicking the checkmark. –  biogirl Mar 11 at 16:56
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What you call influenza isn't a specific virus which is always the same, but a virus that has numerous different strains. Flu virus is constantly alive on this planet, and there are numerous different types, such as the ones which infect humans, the ones that infect birds, and occasionally a virus that mutates to infect humans although it shouldn't as it infects birds only.

Viruses evolve very quickly. The strain of flu virus which was rampant last year definitely won't be the one to look out for this year. What scientists are doing is a very difficult job - they're tracking the progress of different flu virus strains and trying to make an educated guess about the strain or strains which might spread the most during the flu season. And then they come up with a flu vaccine which is a mix that targets the several strains that were identified as being the biggest threat.

It's a hit or miss kind of thing, and it's quite possible that the scientists get it wrong, or not necessarily wrong, but something happens in the virus evolution process that renders this year's vaccine useless.

Also, it's possible to get a flu vaccine and still get flu - if you happen to come in contact with a strain that wasn't targeted by the vaccine. Viruses evolve very very quickly, so vaccine isn't failsafe, virus can evolve in some other person, you come in contact with the virus and get infected despite being vaccined against the original strain.

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I hear you that viruses evolve very quickly. It's interesting that the combination of viruses we call "influenza" seems to change so much more quickly than polio and measles (see comments on @AndroidPenguin's answer above). –  kuzzooroo Mar 12 at 0:15
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