If variola virus didn’t cause deadly outbreaks until about 500 years ago, what was behind the earlier plagues attributed to smallpox? “That’s the million-dollar question,” Poinar says. One possibility, researchers say, is another virus with similar symptoms, like chickenpox or measles.
Another puzzle: If smallpox virus wasn’t around until the late 1500s or so, how did epidemics of smallpox or a similar disease strike indigenous people in the Americas before then? Researchers think those outbreaks might have been triggered by a less virulent ancestor of variola that Europeans had become immune to before they carried it to the New World, where people were susceptible to it. Meanwhile, in Europe, the virus mutated into something more lethal, causing terrible outbreaks, one of which took the life of that Lithuanian child.
It is possible that the family of such virus strains intermittently grows a lethal strain, and that they all have pretty similar effects when they do--as the article suggests. It seems quite a coincidence, though. There's a simpler explanation. Either the researchers' model or their procedure is screwed up.