Firstly, most of the African runners you see are from three regions: Nandi, in Kenya, and Arsi and Shewa in Ethiopia, near the Rift Valley. These are high altitude places, which has lead to some thought that there might be a genetic predisposition to being better at endurance sports in these peoples - lower oxygen levels meaning higher red blood cell count and all that.
Genes and diet have both been considered but there isn’t a lot of evidence to support it as a theory.
East African runners tend to use less energy than caucasians, and the explanation generally given is that they carry less weight on their feet and ankles due to body shape.
Training is also apparently different in East Africa - a sort of quality over quantity approach. There is also the fact that 50-70% of East African elite athletes ran long distances to get to school every day as children.
The influence of biology is hotly debated, but it’s clear that the stereotype is self-perpetuating and that an endurance running culture (and therefore infrastructure, coaching programmes, etc) might form and lead to future success.