Upload a cover letter as a separate file in the online system.
The cover letter should address the following questions:
Why is this manuscript suitable for publication in PLOS Computational Biology?
Why will your study inspire other members of your field, and how will it drive research forward?
You may recommend a suitable Associate Editor to handle your submission; however, the editors reserve the right to contact an alternative—either from the board or a guest editor.
The cover letter will only be available to the editor and the journal staff.
From the PLOS submission guidelines for cover letters:
Example cover letters from the lab: