Sorry for the delay in responding... In all honesty, your problem really lies within the statement WHERE post_status = 'publish' AND ... How many posts does your blog have, and I would honestly refer you to the MySQL website along with, your themes 'forum' and see if anyone else has run into this problem...
The search from publish could be really slow on a large website and not having your MySQL tuned properly... I was working on one of my sites that used the somewhat the same statement to search for videos (believe it or not) through all my posts, almost four years with, extrapolate the appropriate data and send it to a "slider" in one of the sidebars... What I did was used the Wordpress codex pages and rewrote the query to reflect 'specific' categories however, I see in your case it is 'comments'... Is this by some chance a spam plug-in, would you have a link to the slow page? I am going to guess this code exists within your single.php or possibly a comments.php It would be nice to see the source code via a we page link (will do)...