http://www.digitaljournal.com/article/344575

Op-Ed: Virus with its own immune system discovered

Posted Mar 1, 2013 by Paul Wallis
Virology isn’t a subject for the weak-minded. The world’s most changeable forms of life keep coming up with new tricks, and this one, an actual arsenal of immune capability of viruses against immune responses, is a real eyeopener.
 Four DNA strands come together in this model  built using data from x-ray crystallography
"Four DNA strands come together in this model, built using data from x-ray crystallography"
Jean-Paul Rodriguez
National Geographic has an article by virologist Carl Zimmer which clearly explains how effective immunity to viruses is acquired:
… About forty percent of bacteria carry a set of genes known as CRISPR. When a virus invades these bacteria, they capture fragments of its DNA and insert them into their CRISPR genes. The bacteria then use those captured fragments as a guide for building weapons against the virus.
Here’s how this weaponizing works. In order to turn a virus’s genes into new virus proteins, a microbe must first make a copy of the gene in a molecule called RNA. CRISPR genes can produce RNA molecules with a matching sequence. They grab onto the virus’s RNA and prevent them from being turned into proteins. The virus factory grinds to a halt.
(Note: Read Zimmer's article in full. He covers a lot of other very interesting related issues. I'm focusing on the viral immune system in this article.)
Some weapons interfere with viral reproduction very effectively. The article describes these CRISPR genes encoded in the bacteria as “viral barcodes”, and provides a pretty jaw dropping, excuse the expression in context, case in point:
Last year, scientists at Indiana University surveyed the bacteria in people’s mouths and discovered 8,000 different viral barcodes–many of them corresponding to viruses scientists have yet to discover.
Before we get on to the virus with its own immune system, a few points:
1. That many “barcodes” means a very high rate of incidence of infection over time. This is essentially a genetic library. Bacteria pass on their immune capabilities to their next generation, so this cumulative total is very important. It'd be interesting to see how these CRISPR counts develop over time.
2. 8000 specific codes also means a very wide range of different viral infections. Each code is for a specific viral infection. Imagine 8000 simultaneous infections.
3. Mouth flora is one of the body’s more effective defences against infection, so these very well equipped bacteria are doing a pretty good job, by any standards. Makes you wonder if antibacterial mouthwashes are such a good idea after all.
4. Commensal bacteria also send signals to the body’s own immune system. They’re very useful in this regard, and add an extra layer of protection against infections.
5. It'd also be interesting to see how the stored CRISPR codes change over time. Do they become redundant? Are they modified in new generations? It'd be nice to know, because it'd also be a good tracking system for viral exposure in human populations. Might even be a good way of tracking some viral mutations.
(A pithy insight- Elsewhere the article reports that CRISPR is so good at managing genes it's now being used by science as an efficient DNA editor. It reads like it's a toolkit.)
The virus with its own immune system
Meanwhile, the viruses have come up with their own countermeasures, with some interesting ramifications. Developing a way of avoiding the bacterial defences also gives viruses a major advantage over competing viruses. It makes perfect sense for any organism to evolve a defence, and this one is obviously well worth evolving:
Now some proof of the evolutionary advantages of making your own defences: A study of 15 viruses that prey on the bacteria that cause cholera showed that all but one species of virus died out in 10 years and that species became the only predator on the cholera bacteria- Yes, it’s the one with its own immune system.
This virus, called ICP1, has its own full set of CRISPR genes. The virus’ CRISPR genes defend and basically “jam” and counteract the bacterial defences in the same way the bacterial CRISPR blocks them.
Proving this discovery involved mutating bacteria so they had a different CRISPR profile. The mutant bacteria were effective against the viruses and destroyed the majority of them. The trouble is that a few viruses survived, and these survivors adapted to the new defences, able to attack again.This also pretty much proves the point that the CRISPR strategy is the more effective option for both viruses and bacteria.
National Geographic should get an award for dry humor at this point:
The ICP1 virus didn’t evolve its own CRISPR genes on its own, the scientists conclude. It stole them. … The CRISPR genes in ICP1 most closely match those of the bacteria that cause bubonic plague.
Nice to know, isn’t it?
That lineage of bacteria went clear around the world during the plague days, and it’s still around in some places.
What’s also new about this process is that it’s one of the first indications of the level of adaptability of two very different types of organism. Some biologists even dispute that viruses are even a form of life, but let's face it- there aren’t many rocks that evolve like that.
Another point to consider is that every other form of life on the planet has a stake in this global war. If some particular types of viruses evolve a way of beating all countermeasures, they win, and life on Earth can never be the same. The bacteria that support the growth of plants and the inner bacteria of animals could be decimated by immune viruses, and that would literally change the face of the world.
If the bad bacteria beat their viruses, it also means that a lot of very nasty bacteria have escaped from at least one of their most effective natural controls. I doubt if anyone would want to guess how effective viruses are at controlling populations of the truly deadly bacteria in terms of percentages, but it’s a safe bet that they do have a significant impact.
Bear in mind that generations of evolved viruses and bacteria are being born all the time. Also, consider that if either side in this war wins, one likely result for everything else on the planet is a choice of deadly organisms on the rampage.
It also creates an issue for what seems to be a very good idea- Using friendly viruses to manage mean diseases. This is now a working possibility, but- We know how resistant some bacteria can be to antibiotics, what happens if they become resistant to viruses, too?
Simple, eh?
Just to be on the safe side, start being very nice to your local fungi and consider turning into a rock.