The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution

Department of Organismic and Evolutionary Biology, Harvard University, United States
Department of Physics, Harvard University, United States
Biological and Biomedical Sciences, Harvard Medical School, United States
Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, United States
Department of Genome Sciences, University of Washington, United States
Medical Scientist Training Program, University of Washington, United States
Howard Hughes Medical Institute, United States
NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, United States
Quantitative Biology Initiative, Harvard University, United States

Feb 21, 2023

https://doi.org/10.7554/eLife.83442

Open access
Copyright information

Peer review process
Decision letter
Author response

Peer review process

This article was accepted for publication as part of eLife's original publishing model.

History

Version of Record published February 23, 2023
Accepted Manuscript published February 21, 2023
Accepted February 6, 2023
Preprint posted September 14, 2022
Received September 13, 2022

Go to the preprint

Decision letter

Jos W van der Meer

Senior and Reviewing Editor; Radboud University Medical Centre, Netherlands

Our editorial process produces two outputs: (i) public reviews designed to be posted alongside the preprint for the benefit of readers; (ii) feedback on the manuscript for the authors, including requests for revisions, shown below. We also include an acceptance summary that explains what the editors found interesting or important about the work.

Decision letter after peer review:

Thank you for submitting your article "The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution" for consideration by eLife. Your article has been reviewed by 2 peer reviewers, and the evaluation has been overseen by a Reviewing Editor and Jos van der Meer as the Senior Editor. The reviewers have opted to remain anonymous.

The reviewers have discussed their reviews with one another, and the Reviewing Editor has drafted this to help you prepare a revised submission.

Essential revisions:

As was brought forward by reviewer 2, we would like to see more of a dive into the peculiarity of the finding with respect to epistasis. More details can be found in review #2 below.

Reviewer #2 (Recommendations for the authors):

In addition to the comments in my public review, I wanted to emphasize more interpretation of the specific results. This project offers an incredibly impressive amount of labor, and from my lens, seems to be analyzed properly.

Like I suggested, I'd prefer to have the epistasis results couched with respect to other modern studies of epistasis in proteins (even in SARS-CoV-2). And I would the methods used to detect epistasis to be embedded in greater modern discussions of how higher-order epistasis shapes landscapes of various kinds.

All in all, a terrific study.

https://doi.org/10.7554/eLife.83442.sa1

Author response

Essential revisions:

As was brought forward by reviewer 2, we would like to see more of a dive into the peculiarity of the finding with respect to epistasis. More details can be found in review #2 below.

In this revision, we have added a paragraph to the main text and more information in the methods section, as requested by the reviewers. We have also corrected an error in our preprocessing pipeline, and updated figures to reflect these slight modifications.

https://doi.org/10.7554/eLife.83442.sa2