The immune system usually fights the virus, but sometimes, a sneaky virus turn the tables against the host and uses its immune system against itself:
Bacteria often carry repetitive genetic sequences called CRISPRs, which protect them against viruses.
When a bacterium is attacked by a virus, it copies a small piece of the virus's DNA and stores it among the CRISPRs. The bacterium will then be better at fighting off the virus: the bacterium can acquire resistance, just like a human acquiring resistance to a disease.
The CRISPRs are a library of diseases, storing samples of past infections. If the same kind of virus attacks again, the bacterium is ready. Any viral genes that enter the cell are quickly marked for destruction. [...]
But the war isn't over. Viruses are notoriously adaptable. According to Andrew Camilli of Tufts University in Boston and colleagues, ICP1 has managed to turn the CRISPR system to its own advantage.
Camilli discovered ICP1 in 2011, and found it to be common in cholera bacteria in Bangladesh. The surprise came when his team found ICP1 had its own CRISPRs, and genes for the Cas proteins, probably stolen from a bacterium.
Camilli looked at the genetic samples stored in the virus's CRISPRs, and found that two of them were identical to a section of the V. cholerae genome. Better still, these bits of DNA are involved in other aspects of the bacterium's immune response.
The implication is that at some point, the virus must have stolen part of the bacterium's arsenal and re-programmed it to target what was left.
Michael Marshall of NewScientist's Zoologger has the post: Link