I found a list on antivirus software for ubuntu, and they should be LSD compatible, so they should work on Centos. You can use the link above the check if they are.
The list is here, and wikipedia also contains a list of linux antiviruses.
I am not sure if they all suit your needs, but I know that AVIRA has a command line scanner.
Here are some sample lines of code:
scancl / --defaultaction=ask
scancl /var/www -z --defaultaction=repair,delete