Backdoors are pieces of code that allow attackers to bypass authentication, maintain their access to the server and reinfect files. Some of those malicious files can be as simple as a single line of code, allowing the execution of remote code, or complex algorithms, providing different functions to the attacker.
System shells are type of backdoor allowing the attacker running various, even more complex commands directly within the infected operating system.
Any PHP based web site (often through outdated WordPress, Joomla, osCommerce, Magento, Drupal and stolen passwords).
Cleanup is done by deleting the malicious file, which can be found in your system by searching for system_shell() or system() functions inside your files. Reviewing access logs for non-expected HTTP POSTs can point out the possible infected files.
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