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
Decision letter
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Jos W van der MeerSenior 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.sa1Author 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.sa2Download links
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The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution
eLife 12:e83442.
https://doi.org/10.7554/eLife.83442
