https://orcid.org/0000-0003-0778-3477
Peer Review History
| Original SubmissionNovember 19, 2020 |
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Dear Prof. Su, Thank you very much for submitting your manuscript "Evolution of the interactions between GII.4 noroviruses and histo-blood group antigens: Insights from experimental and computational studies" for consideration at PLOS Pathogens. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations. This study is an additional analysis of the known factor that is associated with susceptibility and infection of humans and noroviruses. They use yeast expression to prepare the capsids of several strains from a recent common lineage (GII.4) of human noroviruses that has become widespread around the world. They perform binding studies to the different blood group glycans, showing increasing binding over time of evolution of the viruses. They model the docking of the glycans into the structures of the viruses based on the sequences and known structures of related viruses binding to the different blood group antigens. The data is similar to previous studies, but adds additional approaches as well as details from the more recent viruses. That data supports the general connection of the affinity of binding to the increased spread of the viruses, but there is no direct connection back to the disease in vivo, and data is mostly suggestive. The manuscript is clear and well presented, and the data appear to be fine as far as they go. Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. When you are ready to resubmit, please upload the following: [1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out [2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file). Important additional instructions are given below your reviewer comments. Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments. Sincerely, Colin Parrish, Ph.D. Editorial Advisor PLOS Pathogens Raul Andino Section Editor PLOS Pathogens Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens *********************** This study is an additional analysis of the known factor that is associated with susceptibility and infection of humans and noroviruses. They use yeast expression to prepare the capsids of several strains from a recent common lineage (GII.4) of human noroviruses that has become widespread around the world. They perform binding studies to the different blood group glycans, showing increasing binding over time of evolution of the viruses. They model the docking of the glycans into the structures of the viruses based on the sequences and known structures of related viruses binding to the different blood group antigens. The data is similar to previous studies, but adds additional approaches as well as details from the more recent viruses. That data supports the general connection of the affinity of binding to the increased spread of the viruses, but there is no direct connection back to the disease in vivo, and data is mostly suggestive. The manuscript is clear and well presented, and the data appear to be fine as far as they go. Reviewer Comments (if any, and for reference): Reviewer's Responses to Questions Part I - Summary Please use this section to discuss strengths/weaknesses of study, novelty/significance, general execution and scholarship. Reviewer #1: In this article, the authors study the interactions between different types of histo-blood antigens (HBGAs) and virus-like particles of nine representative genotype II.4 strains of Norovirus. This work aims to understand binding affinity evolution at the structural (atomic) level. Indeed, the biding activity of HBGAs increases along the evolution of genotype II.4. The study combines both experimental and computational methods. In particular, the authors used molecular dynamics and molecular mechanic/generalized born surface area calculations to interpret enzyme linked immunosorbent assays. This allows the authors to interpret mutations consequences for binding affinity. It is a very interesting work. The results are clear and well described. The methods are rigorously applied with correct interpretation. This work is suitable for the audience of Plos Pathogens. ********** Part II – Major Issues: Key Experiments Required for Acceptance Please use this section to detail the key new experiments or modifications of existing experiments that should be absolutely required to validate study conclusions. Generally, there should be no more than 3 such required experiments or major modifications for a "Major Revision" recommendation. If more than 3 experiments are necessary to validate the study conclusions, then you are encouraged to recommend "Reject". Reviewer #1: (No Response) ********** Part III – Minor Issues: Editorial and Data Presentation Modifications Please use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. Reviewer #1: Minor point: the authors indicated p25 line 531 that 100 snapshots were used to compute the binding free energy for each simulation. However, in figure 4B, the curves presented do not take account of the statistics. I guess the means are plotted but the authors should show error bars. It would also be informative to present the RMSD for each molecular dynamic simulations in the SI. ********** PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Figure Files: While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org. Data Requirements: Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5. Reproducibility: To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols References: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. |
| Revision 1 |
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Dear Prof. Su, We are pleased to inform you that your manuscript 'Evolution of the interactions between GII.4 noroviruses and histo-blood group antigens: Insights from experimental and computational studies' has been provisionally accepted for publication in PLOS Pathogens. Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests. Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated. IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript. Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS. Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Raul Andino Section Editor PLOS Pathogens Raul Andino Section Editor PLOS Pathogens Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens *********************************************************** Reviewer Comments (if any, and for reference): |
| Formally Accepted |
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Dear Prof. Su, We are delighted to inform you that your manuscript, "Evolution of the interactions between GII.4 noroviruses and histo-blood group antigens: Insights from experimental and computational studies," has been formally accepted for publication in PLOS Pathogens. We have now passed your article onto the PLOS Production Department who will complete the rest of the pre-publication process. All authors will receive a confirmation email upon publication. The corresponding author will soon be receiving a typeset proof for review, to ensure errors have not been introduced during production. Please review the PDF proof of your manuscript carefully, as this is the last chance to correct any scientific or type-setting errors. Please note that major changes, or those which affect the scientific understanding of the work, will likely cause delays to the publication date of your manuscript. Note: Proofs for Front Matter articles (Pearls, Reviews, Opinions, etc...) are generated on a different schedule and may not be made available as quickly. Soon after your final files are uploaded, the early version of your manuscript, if you opted to have an early version of your article, will be published online. The date of the early version will be your article's publication date. The final article will be published to the same URL, and all versions of the paper will be accessible to readers. Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Kasturi Haldar Editor-in-Chief PLOS Pathogens orcid.org/0000-0001-5065-158X Michael Malim Editor-in-Chief PLOS Pathogens |
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