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TLDR Finances
So I redeemed a Delta flight via Virgin Atlantic with Amex MR and CIti ThankYou points, and paid the taxes with my Chase Sapphire. Am I covered under Sapphire's trip protection?
Yes.
To be perfect clear, the origin of the miles/points is never a factor. The only factor considered for the coverage is if you use any qualified card to pay for the rest of the trip (i.e. tax and surcharges).