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I found a solution to add rel="nofollow" to comments. My theme maker gave me this hack that you can add in functions.php (no guarantee it will work for everyone, might depend on your theme):

function add_nofollow_to_comments_popup_link() {
    return ' rel="nofollow" ';
}
add_filter( 'comments_popup_link_attributes', 'add_nofollow_to_comments_popup_link' );