I would do it by keeping the replies in the Comment table, but having a separate table to link the Comments, thus:
CommentID
InReplyToCommentID
So that if Comment 47 is a response to Comment 13, then there'll be a record in the ReplyTo table:
CommentID InReplyToCommentID
47 13
This has the advantage of being small, and not requiring multiple organisations for storing the same sort of information, as well as not affecting any existing systems.
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