Honestly, that's probably close. It's just a question if all the people infected have nanites. Miles Lanier doesn't iirc.
Miles Lanier doesn't have any nanite enhancements, but he does have cyberware. I remember reading somewhere, cybertechnology I think, that they use nanites to connect and maintain the links between the meat and the ware. Could be he went in for maintenance and in the process, one of the e-entities hijacked the process. Not enough to immediately take control, but enough to establish a "beachhead". Then slowly, as Lanier connects to the matrix, it begins mapping the brain, then starts making modifications. Eventually, it makes enough changes that it can start giving the victim sort of "post hypnotic commands", where the subject is asleep, he will automatically connect to the matrix. Further changes are made, eventually allowing the entitiy to actually "possess" the victim. Then its a matter of taking full control, if possible.
Same could be said for Leonization treatments, I remember reading somewhere that nanites are used in the procedure. Another kind of freaky idea is that one article from stormfront about the advertising nanites on the pamphlet. Could suggest that someone/thing is actively "recruiting".