Imho once you have a trojan how can you ever be sure that your system is not infected in ways you do not know about. root kits etc.
If it is possible I would back up your pictures and music (scan with AV, etc) then reinstall the OS. You did make a system recovery disc? or maybe you had a nice oem that bundled a recovery disc with your PC.
How did you discover the virus? Did it come up on a system scan of your anti-virus? and your AV would not quariteen or remove the infection?
According to this site "Trojan.Agent is not a threat in itself, it is a fake threat displayed by rogue anti-spyware programs. These programs use this and other scare tactics to get the user to buy the full version of the fake spyware removal programs." Programs related to Trojan.Agent should not be trusted under any circumstances and should be removed upon detection.
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These forums (like the link above) can be really helpful for dealing with this sort of thing. Personally I use Linux and a OSX and have Never had a problem with a virus or spyware. You don't need to be an expert to use Linux anymore either. check out Ubuntu .
repair your windows or install a fresh copy, make sure u save the files that u need before doing this.
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Other people asked questions on various topics, and are still waiting for answer. Would be great if you can take a sec and answer them