One contemporary National Autonomous University of Mexican epidemiologist, Rodolfo Acuña-Soto
, argues that mortality due to imported diseases was compounded, or even dwarfed, by mortality due to a hemorrhagic fever native to the Americas, one which the Aztecs called cocoliztli
"The native population collapse in 16th century Mexico was a demographic catastrophe with one of the highest death rates in history. Recently developed tree-ring evidence has allowed the levels of precipitation to be reconstructed for north central Mexico, adding to the growing body of epidemiologic evidence and indicating that the 1545 and 1576 epidemics of cocoliztli (Nahuatl for "pest”) were indigenous hemorrhagic fevers transmitted by rodent hosts and aggravated by extreme drought conditions (...) The disease described by Dr. Hernandez in 1576 is difficult to link to any specific etiologic agent or disease known today. Some aspects of cocoliztli epidemiology suggest that a native agent hosted in a rain-sensitive rodent reservoir was responsible for the disease. Many of the symptoms described by Dr. Hernandez occur to a degree in infections by rodent-borne South American arenaviruses, but no arenavirus has been positively identified in Mexico. Hantavirus is a less likely candidate for cocoliztli because epidemics of severe hantavirus hemorrhagic fevers with high death rates are unknown in the New World. The hypothesized viral agent responsible for cocoloztli remains to be identified, but several new arenaviruses and hantaviruses have recently been isolated from the Americas and perhaps more remain to be discovered. If not extinct, the microorganism that caused cocoliztli may remain hidden in the highlands of Mexico and under favorable climatic conditions could reappear."
See Megadrought and Megadeath in 16th Century Mexico