Why are you using a Python virtual environment? Do you need Python3 in checkmk 1.6?
Checkmk brings its own Python interpreter and the site user is able to install Python modules with pip install.
If that does not work you will need to create a wrapper script that enables the virtual environment and executes gvm-script. This wrapper should be placed in $OMD_ROOT/local/lib/nagios/plugins for checkmk to find it as an active check.