Last year PCI DSS 1.2 was released changing the intent of the controls required for anti-virus software. In version 1.1 anti-virus software was only required for systems commonly affected by viruses and excluded UNIX based operating systems and mainframes. Version 1.2 now requires all operating system types commonly affected by malicious software be protected and removes the exclusion for UNIX and mainframes. These changes now open the requirement for protection from "malicious software" such as worms, trojans, adware, spyware or any "malicious software".
In the past, it was though Linux servers were safe from viruses but recently hackers have been taking advantage of this false sense of security. Some researchers point out that 70% of attacks on Linux honeypots were infected with a 6 year old virus (RST-B)* and used as command and control points for botnets.
*RST-B is a backdoor malware runs on Linux/UNIX platforms and infects ELF files in the current and /bin directories. This Linux backdoor and virus compromises system security by allowing remote users to manipulate and access infected machines. If executed as root, it will start processes listening on two network interfaces which provide a remote root shell.