The end of the second season was very good. That character with the sword and zombie entourage looked mental.
Going back to the original Q, Rick explains near the end of the episode that everyone is infected (a carrier of the virus) and that the chap in the lab compound from the first season told him this. The virus must only take hold upon death.
I also agree that the second season was not as good as the first. My main gripes were:
1) Living in this house on a farm.... everything happened in and around the farm, which wasn't very exciting. the whole searching, travelling, holding on for hope and not knowing what was round the corner was lost with them just camping out in one location;
2) Everyone's reactions to each other’s actions, however insignificant or unavoidable were blown well out of proportion. Characters take it in turn to act completely irrationally then totally rationally. That was very frustrating.