This is a real helpful video on this topic: https://youtu.be/JEYh5WACqEk
But the tl;dr version is that truly awful diseases like small pox(one of the major diseases used to kill native americans) really only pop up and continue to thrive when you have domesticated animals and high population density. Neither of which the native americans had a ton of.
As an additional factor, Europeans were well versed in biological warfare and utilized those principles to intentionally spread disease among native american populations(small pox infested blankets were given to native americans when the Europeans knew to burn them to prevent further spread)
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