PHP has IMAP functions that can read POP3 mailboxes. You would want to combine those with a cron job for frequent polling.
Some mail servers also offer triggers to run when mail comes in - you could create a trigger that calls a PHP script, passing on all the details of the incoming message. If you have access to your server and can implement this, it might be easier to work with because you don't have to connect to the POP mailbox yourself in your script.
If you have a POP3 mail box with good spam checking, this might work - although you would, as Naivists says, of course have to find a method how to identify the target thread reliably.