Some ideas:

• Move the prepare out of the while loop. No need to prepare the same statement more than once.
• Use placeholders to get rid of SQL injection problems, and to improve performace by allowing to cache the prepared statement inside the database engine.
• prepare the insert statement outside the while loop, and use placeholders, for the same reasons.
• Disable auto-commit, and commit manually every few thousand rows, as recommended by the SQLite FAQ.

Alexander