You should be ok given that EK have interline agreements with most of the Virgin group airlines (ie Virgin America, Virgin Blue/Australia etc).

Just make sure you double check the final destination airport code is on the bag tag, especially if you are flying out of an airport which uses contract check-in staff.

If the initial response is no, check with an EK supervisor...good luck. Let us know how you get on. Its a good data point to have.