You’re not alone in experiencing an extended recovery from an “ordinary” GI bug. I’m not sure it’s pouchitis, though, or at least not the usual kind. I’ve had the same experience, even though I’m always on Cipro and Flagyl, and eventually things seem to settle down on their own. If/when my Cipro and Flagyl *really* stop working permanently I expect the next step to be one of the biologic medications, perhaps Humira or Entyvio. A number of folks here have successfully made that transition, some with a biologic alone and some with combination therapies.

Are you symptoms the same as normal pouchitis when a virus has brought it on? I know mine have been - shallow cough, cramping, malaise, feverish (with no fever), urgency, etc. 

I'm guessing it's just going to have to take its course. Sucks though in the interim. 

Everyone is a bit different, so it’s hard to tell except retrospectively. Since we don’t really know what causes occasional bouts of “normal” pouchitis, it’s reasonable to imagine that some GI disruptions could lead to it. If it clears up on its own then it’s probably not “normal” pouchitis, just a slow recovery from the GI bug. People vary in how willing they are to try a course of antibiotics, and how willing they are to put up with the symptoms without taking action - personal preference matters here.