With the ravage of the infection surely some of the more isolated communities could leave behind children.
Given they were young enough at the time they were abandoned it is not unheard of for them to adapt to a pack ect of wild pokemon as a family and travel with them.
These humans would be able to understand general poke in exchange for being illiterate and being unable to speak human languages, any pokemon travelling with them would not have been captured (by them at least) but rather they would operate as a sort of family until they fail to pick up on instinctual pokemon behavioral clues.
This means younger human characters (no older than teenage) could be introduced without worrying about the screening for humans to return to the infected regions, they never left. On the other hand any weapons they possessed would probably be limited to no more than a sharp stick or anything they may have looted from human houses.
As an ingame example N was raised by pokemon in the wild for a portion of his early life without harm, though being raised by more violent species may be impossible.