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Most, if not all, animals have endogenous viruses i.e., copies of parts of or complete retro-viral genomes in their chromosomes. Man, for example, has in the order of 100 000 bits and pieces of retrovirus, distributed on all chromosomes. Most of these bits are grossly defective but in man about 50 can encode a protein. There is evidence several coding endogenous viruses can recombine and start an infection. I believe these coding endogenous viruses contribute to human disease. Indeed I speculate, they are the most important limitation on size and longevity of the members of a species: both these parameters are roughly proportional to the chance of making a replicating virus. In the following I will try to argue for the importance of coding endogenous viruses.
If the presence of retroviral sequences does not lead to replicating virus the situation is mostly fine. However, as soon as a virus starts replicating in an individual, the mutational level in the animal increases dramatically, by way of insertion of viral genomes at unusual places, and the animal in part loses control of its genome. This is known to result in cancer, and I believe in autoimmune disease.
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