I read about the mimivirus it mentions in the article a few years ago, and it mentioned that was one hypothesis. Another is that it went the other way around; before cells were invented life was just increasingly complicated self-replicating molecules and cellular life evolved out of them. In that case the virus-like ancestors would have evolved to prey on their self-sustaining descendents.

I think the uniqueness of this virus' genes suggests that whichever direction it happened, it happened very early in the history of life.