The API and FQL comment table have been updated to support this new feature. The Facebook API now supports different "views" of social comments. The views are broken down into 1. top level view 2. Replies 3. Comment Stream.
For Pages and Profiles with 10k+ views, Facebook admins can opt-into Replies through the Page admin panel in the Manage Permissions section. All Pages will have the feature enabled on July 10, 2013. In the beginning, this will be limited to desktop users only--mobile will be enabled in the future, according to the company.
SOURCE: https://www.facebook.com/notes/facebook-journalists/improving-conversations-on-facebook-with-replies/578890718789613