how to protect
What do you mean from virus? Please consider that there are major differences between Viruses, Trojan horses, worms, Hacks and etc.
Viruses are running on a system to distribute, but usually servers do not run any unspecified programs (except of server softwares) also while servers transfer viruses they don’t infect themselves. But if there is a security vulnerability (security hole); the system is ready to be hacked or be infected by Trojans, if you want to protect yourself applying latest stable softwares is the resolution. (due to known security holes)
WHM/CPanel has a built in update which can be used to protect the box, however has quick security check and Trojan scanning too, also by using fronted firewall and building a DMZ you can add more security and convenience and continuous monitoring of the box is the key element of security.