Q: How do I write a cover letter for a revised manuscript?

Actually, you don’t need to provide a cover letter for a revised manuscript. A cover letter is needed only at the time of submitting the first version of a manuscript.

However, in this case, the situation is not very clear. It seems the journal editor had a look at the manuscript and sent it back to you for changing it (so as not to be similar to your earlier manuscript). That is, the manuscript was not sent for a peer review. [If the manuscript had come back with changes from a peer review, in the revision mail, you would need to talk about the changes you made (or did not). But you would not need a cover letter for this.]

So, if the editor asked you to change the manuscript and submit it again as a new manuscript, you could write a cover letter again. In a cover letter, you need to talk about how your study is novel and how it’s relevant to the journal. In your case, you may also need to talk about how it now distinctly differs from your earlier work.

You will find more information on writing a cover letter, including a template, in the following resources:

• 10 Tips to write an effective cover letter for journal submission (Download - cover letter template)
• Dos and don'ts for a great cover letter
• Should a cover letter be submitted as a document with a manuscript or as an email?

All the best for the (revised) submission!