Open disk maangement using run--> diskmgmt.msc and note the disk number of usb pendrive.
Say disk 1.
Run below command using virtualbox command line.
VBoxManage internalcommands createrawvmdk -filename C:\usb.vmdk -rawdisk \\.\PhysicalDrive#
Replace # with disk id for example PhysicalDrive1 for disk1.
Now, usb.vmdk contains a reference to the usb flash drive.
It need to connected still.
If you want a complete copy of the disk then use the clone command and it will generate a new disk with all data but without link to the usb.
VBoxManage clonehd <old> <new> --format VDI
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