What is telling you that you have viruses? I'm guessing that you have some kind of anti-virus software installed that is identifying some of your e-mail messages as malicious. If so, be aware that you should NEVER allow anti-virus software to delete your e-mail messages! They may not actually be malicious, and if they do happen to be phishing e-mails or contain malware attachments, deleting through anti-virus software will corrupt your mailboxes and won't properly remove the messages from the mail server.
For more information on how to properly remove this kind of stuff, see:
How to remove infected files
Incidentally, what anti-virus software are you using?
(Fair disclosure: I may receive compensation from links to my sites, TheSafeMac.com and AdwareMedic.com.)