If your ISP is telling you that you have a virus, then you probably are sending out spam messages and thus will get blacklisted. It is very unlikely that your server is sending out spam, more likely to be an infected machine. Spammers tend to use their own SMTP engine to send out mail, rather than hoping that there will be one on the infected machine.
Have you downloaded and installed MalwareBytes on all machines (www.malwarebytes.org) - it is a free tool and discovers all sorts of unwanted items.
Lock down your firewall to only send out SMTP traffic on port 25 from your exchange server.
Follow Xmachine's advise in the following EE question - especially to download WireShark and sniff for port 25 traffic from all machines:
Once all machines are checked and clean and no port 25 traffic is detected with WireShark (other than the server), check your reputation on http://www.mxtoolbox.com/b
You will eventually drop off these listings once no more spam is received but it may take a week or so to get clean.
by: debuggerauPosted on 2009-07-08 at 23:59:35ID: 24811206
I think your question subject might be stumping experts since there is no free AntiVirus for Exchange, and even the ones that are, have issues at times..
Any free Antivirus, if set correctly will give you alarms for queued items, but after that, what is it going to do with them?
If it removed them, exchange errors out..
The only free way i know, is to take it offline and run any of a variety of scanners over ALL files and still it will be with limited success as the database store will not be read.