Say, you downloaded a pirated game that happened to be malicious, and you run it on linux using compatibility layers like WINE/Proton, does your linux installation get infected?
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There’s still a layer of abstraction there. Since it requires Wine to run, it wouldn’t be able to run itself in the future unless it’s aware that it’s being run in Wine. Then it would need to set up a way to launch itself via Wine.
How the application is started is a separate question. I don’t know enough about Wine to know if it would install a Windows Service as a user service in systemd or init.d or something like that. But if the app is started it can do anything it wants subject to that user’s permissions.