A cover letter for submission of a manuscript is essentially a letter of request. It should contain your objective - which is to get your paper published, and a few background info about yourself and your study.
Most of the time, journals have specific guidelines about the requirements, maybe it is best that you call your journal and see if they need any kind of information that you need to include in your cover letter.
We are organizing the three-day convention of the Asia Pacific Association of Medical Journal Editors in August. It will feature various workshops and talks about the latest trend and concerns in journal publishing. If you are interested, submit your abstract or register as participant to the APAME 2015 http://goo.gl/wkVTiy
Explain in your own words the significance and novelty of the work, the problem that is being addressed, and why the manuscript belongs in this journal. Do not simply insert your abstract into your cover letter! Briefly describe the research you are reporting in your paper, why it is important, and why you think the readership of the journal would be interested in it.