Highly contagious diseases that're only latent for a short time tend to stay isolated. Only small groups know they're there. Other new diseases are mutations of older ones, brought on by changing population dynamics and environments. Growing coastal algae blooms have been enriched by sewage from land and from ships. They form stew pots, rich in nitrogen and phosphorus.
Bacteria grow in abundance, spread, and mutate as well.
Then whole new strains started popping up, and old diseases reemerged. Bubonic plague failed to do that in the 14th century, and humankind came back stronger than ever. Only in the 16th and 17th-century Americas did brutality and disease do enough damage that the native population never could fully recover. Yet it did survive. Now we turn about and try to exterminate harmful microorganisms.