I thus cannot delete the message from with Mail itself and thereby do a mail-sync-delete via the IMAP protocol to the server and remove both the Mail and the server infected files. Unfortunately as Mail's message files containing the viruses are named xxxxx.emlx where x is a number generated by Mail itself as it creates the Mail database, I cannot match them up to the actual mail messages within Mail.
I thus have the curious situation of a small virus infection (no more than 10 messages in my inbox, which are probably all junk mail anyway), but no way of actually removing them from my system! Thus on the next scan, clamav quarantines the replacement file, which gets replaced, then quarantined, etc. However, as my email is configured using IMAP and the mail server retains the mail, it seems that IMAP sync immediately replaces the quarantined message file with a new copy from the IMAP server. When I upgraded to Snow Leopard (10.6) I also installed ClamXAV to activate OS X's built-in camav antivirus & anti-malware capability, which has successfully picked out a number of email messages containing malware (identified by filename), which clamav then quarantines and I remove/delete.
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