The implication of the viral explanation for endogenous retroviruses (ERVs) is that different kinds of creatures, sharing ERVs in corresponding locations, must have inherited those ERVs from common ancestors.
Something that sometimes confuses the issue is a study that identified one ERV, HERV-K-GC1, that is present in chimpanzees, bonobos and gorillas, but not in humans.doi:10.1016/S0960-9822(01)00227-5 How this could be is explained in the paper. This page presents that explanation in a simplified manner.
The scientific consensus is that gorillas split from the common ancestor of all four species, followed by humans, followed by the chimpanzee-bonobo spit.
How, then, could HERV-K-GC1 be inherited from the common ancestor of all four species by gorillas, chimpanzees and bonobos, but not by humans? Surely there is something wrong here? Doesn't this result contradict the science?
Well, in order to be a contradiction, the result would have to be an impossible one, according to the science. So is the result impossible?
Consider what the viral hypothesis says. An ERV is introduced into a population of organisms by the integration of a retrovirus into a single germ-line cell. Offspring descended from that germ-line cell may or may not inherit that ERV. If any offspring do inherit it, and their offspring too, and so on, that ERV will spread among the population. If it eventually spreads to every individual, we say it is fixed in the population, and every subsequent offspring will inherit it. But all the while it is not fixed, there will exist in the population, individuals with the ERV, and individuals without. Of course, the ERV may eventually die out, as opposed to becoming fixed. In this case, it is the pre-intergration allele that becomes fixed once more. Bear in mind that at the time of writing, there is good evidence that chimps and humans share some 200,000 ERVs and ERV remnants. It is hardly out of the question that such exceptional cases can arise.
This all means that individuals, populations or species that descend from a population that has an ERV that is not fixed need not inherit that ERV.
In other words, common ERVs testify to common ancestors, while the absence of a common ERV does not falsify common ancestry. Look up "incomplete lineage sorting". An example - http://biologos.org/blog/understanding-evolution-speciation-and-incomplete-lineage-sorting
Evidence of unfixed (non-ubiquitous) ERVs in the human population can be found @ Long-term reinfection of the human genome by endogenous retroviruses
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