Though Thomas Rushton already provided a good solution, I'd suggest adding just a new column, InReplyToCommentID in the comments table. Then you have both comments, replies and their relation all in the same table. When you want to find all first Level comments you'll just need to query for comments with InReplyToCommentID being null, with no need to involve a second table.
Unless a reply can be related to more than one comment, I think it's a simpler, more efficient solution.
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