You'll only have a folder named .limewire if you've used much older versions of LW in the past... the preferences folder used to be named .limewire. So don't worry if you don't have one.

The folder that you found was the right one. You should delete that whole folder. Deleting that folder will kill all of your LW preferences - all the settings that you've chosen within LW's options. So, if you're not sure of those, you should go through LW's tools > options & write down all of your settings so that you can re-set everything once you restart LW

If deleting the prefs folder doesn't help, try the other fixes in this thread: If LW Will Not Connect

This is all I could find about the 'virus': Cheat Engine :: View topic - Why does it say infected.

Oops I'm a bit slow