Saturday, September 5, 2009

Hackers Guide to H1N1

I came across a guide to hacking influenza. It creates an impressive analogy comparing DNA to hard disk memory, RNA to RAM, and amino acids to pixels.

The guide discusses how to theoretically hack influenza, making the current strain of H1N1 substantially more dangerous. The post goes on to describe how influenza may well figure out how to perform the aforementioned hack on itself. However, I suspect that if that particular genetic modification made influenza more infectious, it would have already happened by now. If influenza was more infectious, it would infect more people (obviously!), and this would make it more evolutionarily fit because it would be passing on its genes at a higher rate. Thus, since we don't see the hack in the real world, it may be because that particular genetic change makes the influenza less infectious. This same phenomena is seen in HIV. HIV can become resistant to medication, which seems like a genetic advantage, but sometimes when medication is stopped, the HIV infection loses its resistance to the drugs. This is because the non-resistant HIV strain is more evolutionarily fit than the resistant strain and out-competes the resistant strain if it is not hampered by medication. (If this makes you want to stop your HIV meds...DON'T...Go talk to your doctor first!!!)

The guide describes how influenza is made up of genetic compartments and co-infection of a host by two strains of influenza can lead to the creation of novel influenza strains.
Consider what happens when a host is infected by two types of Influenza at the same time. If the genes were stored as a single piece of DNA, there would be little opportunity for the genes between the two types to shuffle. However, because Influenza stores its genes as 8 separate snippets, the snippets mix freely inside the infected cell, and are randomly shuffled into virus packets as they emerge. Thus, if you are unlucky enough to get two strains of flu at once, the result is a potentially novel strain of flu, as RNA strands are copied, mixed and picked out of the metaphorical hat and then packed into virus particles. This process is elegant in that the same mechanism allows for mixing of an arbitrary number of strains in a single host: if you can infect a cell with three or four types of influenza at once, the result is an even wilder variation of flu particles.
This mechanism for genetic variation leads to the most dangerous influenza outbreaks. Imagine two strains of influenza, strain A infects humans and pigs and strain B infects pigs only. Strain A is relatively harmless to humans because we have been exposed to it for a long time and our immune systems have learned how to fight it. Strain B is harmless to humans because it does not contain the required proteins to infect us. However, if a pig was infected by strain A and strain B and the strains shared genetic information, then a new strain, strain C, may be created sharing genetic components from both strain A and strain B. Strain C can be especially dangerous because it may have proteins from strain A that make it infectious to humans, but the proteins from strain B are completely unrecognized by the human immune system, meaning we have little immune defence against strain C. This is what happened with swine flu, avian flu, and the Spanish flu.

Another interesting point brought up in the guide is using influenza as a biological weapon. Theoretically a very scary and dangerous possibility. However, it would be ridiculously difficult to control a weapon like that. Influenza can rapidly spread across the globe, even when the entire world is prepared and trying to stop it. A "surprise attack" with influenza would probably be very difficult to contain and the attacker would be putting himself in grave danger too!

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