cPanel comes with clamav a free virus scanner as a plugin, all you have to do is login to your WHM manager to install it with just a few clicks.
Login to WHM > scroll down to the “cPanel” section > click on “Manage Plugins” > select “install and keep updated ” for clamavconnector and cPanel will install the plugin for you and create the link “Configure ClamAV Scanner” under Plugins section of WHM.
You can use this configuration screen to activate the virus scanner for all or selected users to perform manual scans.
Now to the best part, how to schedule a server wide scan?
First you’ll need to create a temp directory to use as a quarantine area, /tmp/virus for example
# mkdir /tmp/virus
Then add this cron job to crontab to schedule a weekly scan of your /home directory and send the results to your email address (email@example.com)
5 0 * * 0 nice -n 19 clamscan -i -r –move=/tmp/virus /home | mail firstname.lastname@example.org -s “***** Server Name – Infected files *****”