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Rootkits are smart enough to hide themselves as integrated codes/apps. In order to detect such smart injections, you need to monitor some of the specific symptom in your system; like:
In order to prevent rootkit infection in your system, make sure to do follow some of the basic security measures; such as:
First off, examine your own actions for behaviors that are high risk, things like opening attachments on emails and visiting risky sites (which are often risque sites). You might want to also consider keystroke encryption software, which should prevent keyloggers from stealing your passwords, account numbers, etc. It seems like overkill, but as your experience with the rootkit suggests, maybe it is actually just a reasonable level of caution. After all, just because you’re paranoid, it doesn’t mean that they aren’t watching you.