What is confusing is that the article introduces both derivatives (of a function and of a number) as D, when both are definitely not the same thing.
EDIT: that is, the fact that they have the same name and the same symbol is what's confusing.
For better or worse that's very common. A big part of learning to read advanced math is keeping track of the "kind of thing" each variable is meant to be. If you do that, then overloading D is a convenience which illustrates similarities.
But if you're not a professional mathematician then such overloading is terrifically confusing. Actually, I'm fairly certain it still is even for professional mathematicians.
And it's not restricted to primes, it's just defined first for primes and then extended to all integers later.