Having large cities leads to diseases evolving. Something like Smallpox in a small isolated community would result in either everyone dying or developing antibodies to it pretty quickly. It works different in a large city though. There are people moving to the city fast enough for it to have a constant supply of new people to infect.
European settlers brought these diseases that developed in their major cities. Native Americans had no real equivalent. The largest settlement was maybe 10% as large as London, and it was an outlier.
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