Hmm... Well then just include how they changed as the quarantine became harsher and harsher. There was still a period of time where the government cold still keep tack of people during the outbreaks because of various security cameras and scouting teams. (I'll alter some universe lore for this)

During the early stages of the total quarantine (by the time the barrier was being built) there were still security cameras functional within the danger-zone which allowed the authorities to catch glimpses of survivors doing various things (and seeing as we're in a near-future setting, cameras should be littered all over the city). Only recently has the deep-city cameras died down, leaving only the ones at the wall and city edges still functional.

That way you can explain the change in your CS. Does that work? =)