It is mostly just retroviruses that wind up entering the genomes of their hosts. RNA viruses leave a very different imprint: high rates of evolution of the proteins that their proteins interact with, as they race to deactivate their hosts immune responses and their hosts race to deactivate or evade the viral proteins.
There is also a constant, diversifying selection on the components of the immune system (HLA/MHC) that display viral proteins from within cells on cell surfaces for the immune system to be sensitized against. Viruses always evolve to take better advantage of the most common of these alleles, and the rarest of these genes are always selected for in populations as result. The end result is what is called ‘balancing selection’, where rare things become more common and common things become less common leading to the maintenance of great diversity. This is why tissue typing for transplants is so difficult—there is such immune system diversity that most people don’t have the same alleles at these loci as each other. Of course, if something new enters the population that a subset of these alleles isn’t great against, that set of alleles will become less common over time.
It is mostly just retroviruses that wind up entering the genomes of their hosts. RNA viruses leave a very different imprint: high rates of evolution of the proteins that their proteins interact with, as they race to deactivate their hosts immune responses and their hosts race to deactivate or evade the viral proteins.
There is also a constant, diversifying selection on the components of the immune system (HLA/MHC) that display viral proteins from within cells on cell surfaces for the immune system to be sensitized against. Viruses always evolve to take better advantage of the most common of these alleles, and the rarest of these genes are always selected for in populations as result. The end result is what is called ‘balancing selection’, where rare things become more common and common things become less common leading to the maintenance of great diversity. This is why tissue typing for transplants is so difficult—there is such immune system diversity that most people don’t have the same alleles at these loci as each other. Of course, if something new enters the population that a subset of these alleles isn’t great against, that set of alleles will become less common over time.