With the Inca's literally being in the middle of both a apocalyptic small pox epidemic and a civil war and the Aztecs almost immediately undergoing another massive epidemic that academics now think was local rather then Old World in origin
Nitpick: A few academics advanced a theory that it was local in origin. Most pointed to the extreme lethality among natives, and immunity of Europeans, and believed it an old world disease. Then they sequenced the genes and it turned out the latter were correct. It was Salmonella.