This question reveals a misunderstanding of the case for common descent from ERVs. Retroviruses occasionally cross to other species, often distantly related ones, such as from gibbons to koalas. They can also become endogenous in two distantly related species. The presence of the same retroviruses or ERVs is not evidence for common ancestry. It is ERVs in corresponding locations in the DNA of two species that is evidence of common descent - because a bunch of them are highly unlikely (to say the least) to have ended up in corresponding locations, by chance, from independent infections. The only viable explanation is that both species inherited the corresponding ERVs from the same ancestors. Inheritance guarantees corresponding locations. Separate infections do not.
http://jvi.asm.org/content/74/9/4264.full
Gregory J. Baillie and Richard J. Wilkins, "Endogenous Type D Retrovirus in a Marsupial, the Common Brushtail Possum (Trichosurus vulpecula)," Journal of Virology, March 2001 vol. 75 no. 5 2499-2507. http://jvi.asm.org/cgi/content/full/75/5/2499
Robin A Weiss, "The discovery of endogenous retroviruses," Retrovirology, 2006; 3: 67. Published online 2006 October 3. doi: 10.1186/1742-4690-3-67.http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1617120
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