Check disk does not have anything to do with a virus.
If Windows asks you to complete a check disk, then the drive has not been properly ejected at one stage and hasn't been attended to.
There's a file that writes out what's happening with the drive, including when it's been plugged in and ejected. So if the drive isn't ejected, then the file isn't complete, and when Windows sees that this file isn't complete it'll want to do a check disk to ensure nothing's damaged.
Unplugging a hard drive without ejecting a lot of times can damage the hard drive over time. Also, if data is being read or written from/to the hard drive it can become corrupted if not properly ejected.
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