After publication, a letter to the editor says related studies already exist. How should I reply?

"One comment is hard to answer. They write: 'The authors state that no related studies have been conducted to date, but there are some.' They attach three studies with brief descriptions."

"I read the three. The first two are on a similar theme but still quite different. The most recent one has the same topic as ours, but when it was published our manuscript was already under review, so we could not have known about it or cited it."

"Worse, I searched PubMed myself and found two more studies on the same topic as ours. I am unsure whether to mention them myself. It feels like contradicting ourselves, as if our original discussion of the literature was incomplete."

Below is the reply I suggest, followed by my reasons.

We thank [Author A] et al. for adding to the discussion of the background literature. Of the three studies mentioned in the letter, [Author B] et al. and [Author C] et al. evaluated [topic], focusing on [aspect], which differs from the direction of our study. The 2022 study by [Author D] et al. is similar to ours, but it was still under review while we were writing, so we could not have known of it. After a detailed review of the literature, we note that in addition to [Author D] et al., two other related studies used a similar design [references]. [Here, summarize the core points of the three studies, emphasizing how our study differs from them.] Our study remains distinctive because of [features and reasons]. We thank [Author A] et al. for their careful reading, which gave us the opportunity to add to this part of the discussion. Thank you!

The three studies in the letter are easy to handle. For the two that are different, as you said, state how your study differs. For the third, give the dates and say that it really appeared after you submitted, so you could not have known of it.

As for the two studies you found yourself, I suggest raising them proactively. If you don't, the letter writers may write again later, which is a real nuisance. If you raise them first, you can also choose the ground and highlight what is distinctive about your study.

The overall strategy is to use this reply as a supplement to the original paper: prepare the full summary of, and additions to, the related literature at once, and close the gap. This answers this letter and also prevents similar challenges later.

Acknowledge the gap through your actions, but you do not need to write, "We apologize; our original discussion was incomplete." Science is a process of continuous improvement. Having the chance to reply formally in the journal, and proactively strengthening the whole picture when a problem is found, shows a responsible attitude.