Did Smith infect everyone in the Matrix?

One of the answers to another question (Why did Seraph and Sati hide?) raised the point of programs using the backdoors to avoid getting copied by Smith.

I always assumed that Smith infected all the Matrix, based on Neo's talk to the Deus Ex Machina:

The program Smith has grown beyond your control. Soon he will spread through this city, as he spread through The Matrix

Shouldn't we conclude that he really got access to all of the Matrix, including the backdoors? In that case, he would have infected even the Architect, right?

How can we know whether he did or did not?

Answer

Smith does have access to the backdoors:

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But if the Architect stayed in his room then Smith could not have gotten to him because the Architect's room is locked by a special key that can only be used by The One:

The Keymaker: Only The One can open the door. And only during that window can that door be opened.

Additionally, it is possible that Smith did not have access to Mobil Avenue, and even if he did The Trainman has absolute power there ("down here I'm God") and could prevent Smith from copying himself over to anyone in Mobil Avenue. The Trainman is loyal to the Merovingian, so presumably the Trainman, Merovingian, and all the Merovingian's exile minions would be safe from Smith in Mobil Avenue.

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