Because disease are air-borne and as we know, Africa is closer to Europe than is the Americas. So as these diseases were transmitted through air, civilizations in Africa most likely built immunities to these diseases. However, as the Americas were so far away, civilizations in the Americas were unable to build immunities as they were never exposed to such diseases. Also, while the Americas weren't exposed to much zoonotic diseases as we didn't use domesticated animals till the Europeans arrived, from what I know, I believe Africa did. And much of the diseases from Europe that affected the Americas were zoonotic diseases.