Most viruses or trojan's get deleted by an A/V scanner or whatever or the file itself will get deleted, but as part of the program, it leave's a copy of itself in the registry file. I know of a particular one called "AOHell" that was a virus and even after you deleted it, after restart/reboot or shutdown it would come back because it had a file in the registry that did that. Search for removal instructions on symantec or something, as they'll give you step by step on how to fully get rid of it.