Japan had a more enclosed approach to trading than, let’s say, china. And even in both cases, trading had been happening for centuries. In the case of Africa, Iberian cultures were in contact for a long time (eg. Morocco and Spain), and the history of great ancient civilizations was also intertwined (eg. Greece and Egypt).
In the case of America, contact between the two continents was (arguably) never achieved before (or at least in a very long time, if we consider people like Leif Erikson). This made them way more vulnerable to illnesses from the old world. Eurasia and Africa are almost a big unified mass, but America is way further away.
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