I don’t read that passage as meaning there were absolutely no diseases among Native Americans prior to European settlement, but rather, that they were highly susceptible to the particular diseases for which Europeans had generationally-built immunity and brought with them to the “New World.”

Such childhood diseases as measles killed thousands since the Indians had little white-corpuscle resistance built up throughout the ages to disease.

I have read similar accounts about Indians being wiped out with small pox, diphtheria, and/or what the Lenni Lenapes called “ Yellow Fever.” I also have wondered about the high incidence of alcoholism among Native Americans—prior to European influence, they had not consumed alcohol and yet, there are accounts of Indians quickly succumbing to addiction to “Fire Water,” and pawning their resources to get it. Since alcohol converts to sugar in the bloodstream, and since the Native American diet had previously no refined sugars, I’ve wondered if their metabolisms were more prone to alcoholism. But that’s just a pet hypothesis, I’m certainly not a scientist.

But back to your question. Just a guess, but I would imagine that prior to European colonization, the natives must have had their own maladies, or else there would have been no need for medicine men and women. And medicinal plants and herbs would not have been needed. Also no need for sweat lodges. Maybe they even had the same “families” of bacterial and viruses as the Europeans did, but just different strains?

Conversely, I would also imagine that Europeans were more apt to contract diseases for which the Indians had generational immunity. The Jamestown colony comes to mind:

Typhoid fever and dysentery visited Jamestown in recurrent epidemics killing 30 per cent or more of the colonists with each onslaught. Yet Jamestown endured because the leaders of the Virginia Company misapprehended the nexus between the estuarine environment and water-borne, non-immunizing diseases. Each summer, death stalked the town as invading salt water pushed up the estuary and concentrated pathogens in the town's water supply. The prevention of disease and death required the abandonment of Jamestown and relocation into healthier niches, which occurred with the dissolution of the Virginia Company in 1624.

Jamestown Colony

If memory serves, in the Jamestown instance, Europeans died but the Indians had apparently known better than to build a village in a location prone to mosquito infestation. At least now we know the lowly mosquito is one of the most lethal vectors known to man. Still, makes one wonder why we would ever allow Bill Gates to breed them. 🤔. But that’s another topic.