back to article Petascale powerhouse cracks important HIV code

The Blue Waters petascale computer at the University of Illinois' National Centre for Supercomputing Applications is being credited with cracking part of the code of HIV – and possibly helping point the way to new treatments. Simulations carried out on Blue Waters allowed researchers to determine the precise structure of the HIV …

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Ta!

Great article and video. Just the kind of thing I like to read about.

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Astonishing

That is one strange looking virus capsid.

Most of the ones I've seen have been regular polygons or like the Teven group regular polygons with an injector column and tail fibres. Very strange.

But I can't help wondering if chimps are immune why no one had tried developing a vaccine from them in the way smallpox vaccine was originally developed from cow pox.

Let's see what these simulations give by way of treatments.

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Re: Astonishing

I think other primates are immune to the (human) HIV as the HIV virus specifically targets human cells - it has to be it's so specialised and effective. It's not a case that other primates are immune, implying that their immune systems can deal with it, rather that other primates have enough differences in their cells that the human HIV virus has no overall success in infecting them. Other primates have their own versions of HIV and these are not successful in infecting humans as similarly they are too specialised.

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Re: Re: Astonishing

What you say about species-specific viruses makes sense (to me, with nil knowledge of virology).

But viruses do jump species. Think of the various strains of flu that come from birds and pigs, and all the other human ailments that are believed to have been acquired from domesticated animals. When HIV first became widespread there was a credible theory that it was a monkey virus that migrated to humans who were bitten while trapping monkeys for meat.

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Re: Astonishing

While some viruses do jump species, in reality complete jumps are very, very rare. We're all subject to millions of viruses every day, especially those who work or otherwise live with animals, most of these viruses are just not capable of properly infecting humans.

The reason is down to what viruses actually are - to put it in a fairly basic manner, they are a form of life that cannot reproduce on its own and instead has to invade other life (cells) and hijack the mechanisms of these cells in order to reproduce itself - essentially the lowest form of parasite and just like higher forms of parasite, they need to be specialised to do this effectively. From Wikipedia "A virus is a small infectious agent that can replicate only inside the living cells of an organism." (http://en.wikipedia.org/wiki/Virus). To start with, many viruses have to survive in the open environment, or at least outside of a host organism and HIV, for example, is not particularly tough and instead has to be transmitted without using the open environment... which is why, you won't get HIV through (non-intimate or blood sharing) contact with a carrier, through touching what they've touched or inhaling when the carrier has sneezed or coughed. A virus then needs to be lucky enough to find cells that it can utilise, seeking these through the chemical markers of the cells, latching onto these cells, invading them and hijacking the inner mechanisms of the cell. Through all these steps the virus is exposed to being cleaned up, removed, disabled or rendered useless by basic biological and chemical processes or in the case of cross-species, just not able to get far as it will target the wrong genes, mechanisms or chemical signatures. Once in a cell a virus then uses and controls the cell's mechanisms to reproduce itself (some viruses also cause the cells to reproduce, which is the general cause of virus induced cancers). Even once in a cell, if a virus causes the cell to outwardly reflect that the cell is not working correctly then the cell, and the virus in it, will be destroyed by the body's immune system. It's not easy being a new virus!

Viruses mutate a lot, therefore when living continually with animals that are shedding viruses there is always a chance that one virus strain might happen to be able to infect a human. A certain level of "infection" is quite common but usually entirely harmless as the viruses fail at some step of their hijack and reproduction process. For example, the virus might be able to infect a cell but not to reproduce. Even should a virus happen to manage to reproduce itself, it still has to find its way from one human to another, and that's a very different problem as that involves getting out, crossing between hosts somehow (HIV takes shortcuts on this and needs direct transmission) and then evading the immune system and defences of the new potential host.

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Amazing breakthrough

This is great news. I have always thought that the complete definition of a problem is essentially also its solution. With this type of detailed information about the virus, it is only a matter of time before something really approaching a cure is found.

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Re: Amazing breakthrough

There is no money in cures. Treatments on the other hand are a great source of revenue.

HIV might be the exception, due to the high fear, and the fame one would receive for a cure.

I had a good friend die from AIDS in the early 80's before anyone really knew much about it. So I still hope for a real cure.

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What happens if there's ever a virus similar to HIV, but capable of airborne transmission like flu - would we all be up shit creek?

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"we all be up shit creek?"

Unfortunately the only answer is perhaps. If it was as infective, that is to say that there were very few people that had a natural resistance then the population would be decimated without any drug or more likely vaccine breakthroughs - luckily most infections tend to adapt to their hosts and become less aggressive. Let's hope it doesn't happen.

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Unhappy

"What happens if there's ever a virus similar to HIV, but capable of airborne transmission like flu - would we all be up shit creek?"

Actually it looks like Ebola is the one to really fear.

Death is in days, not months or years.

And there were reports that it did become airborne, but the mutation that made so also weakened it to give flue like symptoms. In which case the human race dodged a bullet that day.

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" but the mutation that made so also weakened it to give flue like symptoms. In which case the human race dodged a bullet that day."

If that's is true/confirmed (the link doesn't work) then it actually sounds like a candidate for a vaccine

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I think it's an either/or case. Its unique shape that makes it so effective in human cells (thus it's called *H*IV) has the drawback of being poor at fending off the elements. Similarly to the ebola case. As mentioned, the mutation that allowed ebola to go airborne also made it less infectious, probably because a structure capable of surviving in air also makes it less capable of infection once back inside. The potential bug-a-boo is either (a) a virus that is SIMULTANEOUSLY highly infectious and airborne-capable or (b) a switch-hitter: one that can switch between airborne-ready and highly-infectious depending on the circumstances (various bacteria can switch-hit by hibernating as endospores—can a virus switch similarly?).

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As for an ebola vaccine, that's a longshot. Ebola is a retrovirus, a kind of RNA virus. RNA virii have always been hard ones to nail because, by their nature, RNA virii tend to mutate a lot. It's for this reason we can't nail a virus for the common cold (coronavirus is also an RNA virus).

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Headmaster

>Actually it looks like Ebola is the one to really fear.

>Death is in days, not months or years.

Actually, this is exactly why ebola isn't the one to fear. You see, ebola kills its host far too quickly to spread really efficiently.

Ebola: You get infected in Africa, and you're dead before you even get to the next village, let alone the airport. In most cases, anyway.

HIV: You get infected in Africa, and you die a few years later, and are subclinical (i.e. not showing any signs or symptoms) for much of these years, giving you ample chance to infect everyone you come in all sorts of fun contact with.

From an evolutionary point of view, HIV is much more successful, as it has a larger reservoir of hosts.

As my virology prof explained to us, most viruses tend to attenuate with time - killing your host in particularly gruesome ways is never the parasite's goal, it's living* in the host for as long as possible and spreading to as many other hosts as possible. Therefore, it is entirely possible that in a few hundred years' time, HIV, if it weren't for medicine, would simply cease to be fatal and be more like herpes - a few cold sores every now and then, but mostly just a virus you carry around in your body without suffering any serious harm.

*Viruses aren't really alive, though that is a grey area.

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Boffin

Not up sh*t creek

HIV is a very special case. First, it’s a retrovirus (RNA, not DNA, inside) so it needs reverse transcriptase (RT) to infect (and this is the Achilles’ heel exploited by most current treatments). RT is incredibly sloppy, making an error every thousand base pairs or so, which accounts for HIV’s frantic mutation rate but also means the majority of infections will yield inviable viruses.

Second, there are a lot of major changes that would have to occur for HIV to be communicable via sneezes. (1) it would have to change its target from cd4+ lymphocytes to upper-respiratory cells, which would remove its deadly immune-crushing nature; (2) it would have to drastically alter its chemistry to become less sensitive to temperature and pH fluctuations, both of which wipe out HIV. Changes this drastic surely bring it outside the operational parameters of the virus, as evidenced by the fact we have not seen it appear DESPITE the unbelievable mutation rate of HIV.

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"Ebola is a retrovirus,"

As indeed is AIDS

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Which is why I say virii with long incubations are worse, because for much of that time you can still be a transmitter. That had always been the danger of HIV and AIDS: the fact you can have it and not know it. It's been increased public awareness of that fact that has kept it under control by means of increased testing to catch it at early stages.

IMO, a nightmare virus would be something like a "time bomb": ticking away without your knowledge. It would be (a) airborne or otherwise overly easy to transmit, (b) highly lethal, but (c) with at least decent incubation. I consider us fortunate the closest we've come to a virus that ticks off all three criteria has been the 1918 pandemic, with its iffy (c) qualification.

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Anonymous Coward

Remove the = from the end: http://en.wikipedia.org/wiki/The_Hot_Zone

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Code behind the discovery

NAMD, a Department of Energy-supported code, was the workhorse for this discovery:

http://ascr-discovery.science.doe.gov/synchronized/namd1.shtml

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Happy

Things have come on a bit then. 20 years ago, I was using an 8088 PC and a piece of software called Sarch Latuse to do crystal structure overlay modelling. It took forever, and was frequently wrong so back to square one. Even though I'm involved in technology in my working life, when I you see something like this I stand back and look at what we have now, I'm still staggered at the advances. Shame being nicer to each other cant make the same rate of progress.

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