One of the classic issues on systems running virtualised environments is other virtual machines stealing resource from another , that's assuming that the issue is not caused by the whole environment being under resourced.
Do you access to or information from an performance reporting tools showing I/O, CPU or memory stats?
What is the purpose of the database access is it to verify credentials or to store a record of who has accessed the system.
I am not a mysql person but spent 20 years in supporting Oracle and like others happy to do a bit of support digging especially as I an now retired.