Thank you for using Ubuntu and reporting a bug. This is a known issue and a 
limitation of the AppArmor driver. For now, you need to adjust 
/etc/apparmor.d/abstractions/libvirt-qemu to allow access to host hardware. For 
usb devices (hostdev), adjust this:
  # WARNING: uncommenting these gives the guest direct access to host hardware.
  # This is required for USB pass through but is a security risk. You have been
  # warned.
  #/sys/bus/usb/devices/ r,
  #/sys/devices/*/*/usb[0-9]*/** r,
  #/dev/bus/usb/*/[0-9]* rw,

To be:
  # WARNING: uncommenting these gives the guest direct access to host hardware.
  # This is required for USB pass through but is a security risk. You have been
  # warned.
  /sys/bus/usb/devices/ r,
  /sys/devices/*/*/usb[0-9]*/** r,
  /dev/bus/usb/*/[0-9]* rw,

You will have to add similar entries for PCI devices (pcidev).

** Changed in: libvirt (Ubuntu)
   Importance: Undecided => Medium

** Changed in: libvirt (Ubuntu)
       Status: New => Triaged

** Summary changed:

- virt-manager allows selection of PCI devices for a VM but apparmor is not 
configured to allow access to the PCI device
+ apparmor driver blocks access to hostdev and pcidev devices

** Tags added: apparmor

-- 
apparmor driver blocks access to hostdev and pcidev devices
https://bugs.launchpad.net/bugs/545795
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