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New viruses

Anti-virus programs are not always effective against new viruses, even those that use non-signature-based methods that should detect new viruses. The reason for this is that the virus designers test their new viruses on the major anti-virus applications to make sure that they are not detected before releasing them into the wild.

Some new viruses, particularly ransomware, use polymorphic code to avoid detection by virus scanners. Jerome Segura, a security analyst with ParetoLogic, explained:

“It's something that they miss a lot of the time because this type of [ransomware virus] comes from sites that use a polymorphism, which means they basically randomize the file they send you and it gets by well-known antivirus products very easily. I've seen people firsthand getting infected, having all the pop-ups and yet they have antivirus software running and it's not detecting anything. It actually can be pretty hard to get rid of, as well, and you're never really sure if it's really gone. When we see something like that usually we advise to reinstall the operating system or reinstall backups.”
A proof of concept virus has used the Graphics Processing Unit (GPU) to avoid detection from anti-virus software. The potential success of this involves bypassing the CPU in order to make it much harder for security researchers to analyse the inner workings of such malware.

Rootkits

Detecting rootkits is a major challenge for anti-virus programs. Rootkits have full administrative access to the computer and are invisible to users and hidden from the list of running processes in the task manager. Rootkits can modify the inner workings of the operating system and tamper with antivirus programs.

Damaged files

If a file has been infected by a computer virus, anti-virus software will attempt to remove the virus code from the file during disinfection, but it is not always able to restore the file to its undamaged state. In such circumstances, damaged files can only be restored from existing backups or shadow copies (this is also true for ransomware); installed software that is damaged requires re-installation (however, see System File Checker).

Firmware infections

Any writeable firmware in the computer can be infected by malicious code. This is a major concern, as an infected BIOS could require the actual BIOS chip to be replaced to ensure the malicious code is completely removed. Anti-virus software is not effective at protecting firmware and the motherboard BIOS from infection. In 2014, security researchers discovered that USB devices contain writeable firmware which can be modified with malicious code (dubbed "BadUSB"), which anti-virus software cannot detect or prevent. The malicious code can run undetected on the computer and could even infect the operating system prior to it booting up.

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