Poking around my sources, I'm not sure what I have on this exactly. I found a book or two in my school's library that I'll go check out later today, and give an update for you if it's fruitful.

What I do know is that Wayna Qhapaq, the current ruler of the Inca, was off in the extreme northern fringes of the empire, working on expanding it. This would be modern-day Ecuador or northeast Peru. Hemorrhagic smallpox was starting to make the rounds back at home in Cuzco, and at this news he began to hurry home. However, he too got sick and died while on the way back to his homeland. What really threw everything into chaos is that his chosen heir to the throne, Ninan Cuyuchi, also dies of smallpox around the same time as his father. Wayna Qhapaq had something like sixteen wives and fifty children, only a few of whom were full-blooded Inca. One of those children, Washkar, claimed the throne and ruled briefly, before his half-brother Atawallpa started a civil war.

So in a way, the Inca started a fraternal succession war because of smallpox, heh.

EDIT: Found the source, Noble David Cook's Demographic Collapse from 1981. Not actually all that helpful, he only ever talks about Spanish census taking and epidemics post-Contact. If you're curious how it got handled by the Spanish, maybe I can help, heh.