It's not a literal term, but rather a way of describing how unpopular and "invisible" Greg is. He's at the very bottom of the social ladder, basically the "anti-alpha" or the ultimate outsider.
Think of it like this:
* Alpha: The popular, cool kids
* Pre-alpha: Maybe slightly less popular but still in the "in" crowd
* Pre-alpha minus: Way down there, barely even noticed by the popular kids
Greg's "pre-alpha minus" status highlights his struggles with fitting in and his frustration with being constantly overlooked. It's a humorous way to show how he feels like an outcast in his own school.