How do you know? Modern day viruses and root kits go out of their way to make things look "business as usual"
How do you know? Modern day viruses and root kits go out of their way to make things look "business as usual"
But of those infected systems, we see relatively few that have truly sneaky, invisible-to-the-user malware. Far more that's just a gigantic pain in the ass to remove as it's hooked into everything in order to display ads at the user or rewrite links or shoddy code has destroyed one or more browser or OS components.
On my VPS's I always assume I was already compromised. I never trust my system in current state until I do all the checks including analysis of my logs. I have automated this into certain level but you can never know :-)
People I work with used to say that it is only a matter of time somebody will try something you have not thought about - to be prepared for such situations is the key. But that's just my private opinion.