The three attacks you've mentioned, code mutation, code fragmentation and code concealment through rootkits, are some of latest evolution of new malicious code generation techniques. All are designed to make it harder to detect the virus or rootkit, and take the concept of the polymorphic virus one step further.
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These programs are being designed to stick around undetected for as long as possible on infected systems. Some malware designers use "packers" to encrypt malware to evade detection.
Others use different routines for decrypting the code to create a virtually unlimited number of mutations, such as the Trojan Swizzor did recently.
Swizzor repacked itself once a minute to get past signature-based tools that work only if they know precisely what to block. Swizzor also recompiled itself once every hour.
Zero-day attacks using well-concealed Trojans present a serious challenge to the security professional. Therefore it's very important to rely on a security product or group of products that really stays on top of current threats and vulnerabilities.
Of course, all of the usual steps your customers take to prevent any type malware always need to be taken, and may help prevent some of these exploits.
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