The recent book "1491" By Charles Mann and the sequel "1493" deal with this topic, and that author goes with the extreme estimates that declare the diseases caused a plague that ran ahead of the explorers, decimating the native populations down by up to 90% even before the conquest of the Americas.

This is an extreme view, and the author gives many historical references for it, but it is still being hotly debated as to the extent of this plague.

Latin Americanists and Atlanticists mostly agree with Noble David Cook's estimate of 90% mortality for indigenous Americans from contact to the eighteenth century. Born to Die (206) Diseases did indeed destroy entire settlements, cultures, and ethnicities. The falling native population forced the Spanish Crown to bring in captured natives from outside areas of the Caribbean, starting in the 1520s. They would, it was believed, reestablish the precontact populations and allow for the continuation of encomienda grants. When this failed, along with social change pushed for by Las Casas, African slavery was established in far greater numbers. The implementation of African slavery radically changed how agricultural institutions operated and attracted more and more colonists to the Americas. Furthermore, disease disrupted indigenous political authorities (the Inka were fighting a Civil War when Pizarro arrived because an outbreak of disease from the north created a power vacuum between Atahualpa and his brother Huaskar) and allowed for the Europeans to dominate the Americas piecemeal. The Inka disease event is discussed in Mann's book.