Q: How should I reply to a reviewer who says that I did not address his comments from the first round of review although I did so?

There are two aspects to your query. One, there seems to be some miscommunication, misunderstanding, or misinformation on the part of the first reviewer with regard to your revisions. Two, due to any of the aforementioned gaps, you are concerned that it may lead to a rejection of your paper. Let’s deal with these one by one.

Addressing the gap

Clearly, there is some gap in this situation. While you seem to have made the changes with due care and diligence, you could go through the comments again to ensure that all the comments have indeed been addressed. This is to be certain that the lapse isn’t on your part. If needed, you may also ask a colleague to go through the reviewer’s comments and your responses to them to ensure that you have adequately responded to all of them. If you can be certain the lapse isn’t due to you (or have addressed the gap, if needed), you may write to the editor about this. If needed, you could point to specific instances to show that you have indeed addressed all the comments in the best way possible.

Conflicts between reviewers and authors are not uncommon, and editors are quite used to and equipped for dealing with these. Once the editor realizes that you have indeed addressed the comments satisfactorily, they can share this with the reviewer and seek to assure them of the same. However, for various reasons, reviewers can sometimes be a bit “difficult.” If everyone has the good of the research – and science – as their goal though, they should be able to work toward a resolution. In the worst case, the reviewer may be biased, again, for a variety of reasons. There’s unfortunately little or nothing you can do in this scenario, and will have to leave it to the editor to arrive at a solution.

Aiming for acceptance

You have no doubt worked hard on this paper, and based on the responses from the two other reviewers, believe there is a good chance for the paper to be accepted. The situation with the first reviewer, though, obviously presents a challenge. However, presently, you shouldn’t worry too much about the eventual fate of the paper, but concentrate on resolving the issue with the first reviewer. Once the matter is resolved, the chances for your paper will automatically improve. If the issue is likely to take much longer to resolve though, and you have an academic dependency, you may choose to withdraw the paper and submit to another journal, perhaps even a rapid publication journal to make up for the time taken here. If, in the worst case, the paper is rejected, then too, you may consider modifying it as necessary and submitting to another journal.

All the best for a rapid, amicable resolution!

You may also go through the following resources for more help on dealing with challenging peer review situations:

• Do's and don'ts for responding to peer reviewers' comments
• How to deal with harsh or negative comments by the third reviewer?
• How should I respond to peer reviewer comments that I strongly feel are biased?