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Although I have never tried it and I have no such camera so I have just looked around and found the following.
There is a WITH_XIMEA built option for OpenCV to support XIMEA cameras (check CMakeLists.txt in e.g version 2.4.3). XIMEA has xiQ which is an USB 3 vision camera, the Support subpage mentions OpenCV among other libraries. Here is a page describing the OpenCV building with XIMEA support under Windows.
Here is the install page for Linux (version 2.4.3).
So I would say, yes, USB3 Vision protocol is supported.
