Comment 3 for bug 256880

Wine becoming compatible with Windows up to a level viruses can run is certainly a feature - by implication that Wine is running well. Wine is not designed to distinguish what kind of program it runs, but to run it as the program intends.
However I think this problem of viruses running should be addressed. Even if it isn't damaged by them, Ubuntu shouldn't carry and transmit viruses. And the potential is always there for a Wine-run virus to attack things in the user's home folder, thus becoming a Linux virus. Whether that second option is more likely than a native or cross-platform virus I don't really know, but I can imagine it being so.
Certainly the first at least has happened, and should be addressed.

I don't know how to do it, but checking files with ClamAV (the back end to the aforementioned clamtk) before opening them in Wine sounds like a very good idea. It won't slow down native operations and programs, as an antivirus program on Windows does, but it will protect against Windows viruses running under Wine.