https://orcid.org/0000-0002-4123-3287
Peer Review History
| Original SubmissionOctober 2, 2023 |
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Dear %TITLE% Ghafari, Thank you very much for submitting your manuscript "Revisiting the origins of the Sobemovirus genus: a case for ancient origins of plant viruses" 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. 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, Peter D. Nagy Academic Editor PLOS Pathogens Savithramma Dinesh-Kumar 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): 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: This very interesting study revises the evolutionary history of sobemoviruses by taking into account the TDRP. As a result it is proposed that the origin of this genus, and its initial diversification on infect different plant families, is orders of magnitude older than previously considered. The study is based in all available information on sobemovirus diversity, and uses the most appropriate methodology, and the paper is well written and easy to read. I have only minor suggestion that could improve the text. Reviewer #2: In this interesting and potentially important paper, Ghafari et al. estimate the age of the viruses in the family Sobemoviridae, taking into account the time-dependent rate phenomenon using the Prisoner of War model. The come up with an estimate of about 4 million years for the origin of sobemoviruses, orders of magnitude older than previously believed. They then explore the evolutionary history of this virus family, revealing likely host jumps and major radiation during the Neoltithic period. Such findings are indisputably important for understanding virus evolution. The article is very clearly and well written but, in the opinion of this reviewer, requires a substnatial amendment to become fully convincing, as detailed below. ********** 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: There are no major issues. Reviewer #2: Surprisingly, nowhere in the paper is the Prisoner of War model actually explained. This seems to be a must for the reader to be able to understand what was actually done. An adequate explanation has to be included in the Introduction. Even more importantly, the description of the model in Methods section is overly brief and effectively uninformative. It needs to be adequately expanded including the statistical evaluation of the results. As it stands, the reader simply has to believe the estimates which is not acceptable. ********** 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: 1. Abstract and elsewhere. The authors often refer to the Neolithic as a time frame, which may be confusing and is probably incorrect. The neolithic refers to a period of technical development associated with agriculture, and occurs at different periods in different regions of the world, the 10000 yr PB mentioned is mostly of application to the Near East. As sobemoviruses seem to have “speciated” in different regions of the world (as stated for CfMV and RYMV) the time frame for the neolithic may vary very much. Certainly, neither in West Africa nor in temperate Europe did the neolithic occur 10000 yr ago. It would be thus good to rephrase the corresponding sentences. 2. Lines 111.113. No need to use three independent sentences all starting by “The genome”. 3. Metagenomic sequences. I am surprised that no sequences were retrieved from plant viromes or plant metagenomic data. How is this so? Were plant data bases not searched?, or they were searched and no sobemovirus sequences were found? 4. Line 188. Herbaceous should be substituted by herbivore. 5. Discussion. The uncertainties unavoidably associated to phylogenetic analyses extended back in time, and shown by the huge confidence intervals in Fig. 3a, should be somehow acknowledge in the discussion. Such uncertainties, by the way, do not in the least diminish the interest and novelty of the results, as they are intrinsic to all historic studies. 6. The colours used to indicate host families in Fig. 2b are really hard to see. Perhaps the colours could be used as shadows over the virus name rather than in the letters. Reviewer #2: I suppose this is too much to ask but to this reviewer, this work would have been far more interesting and compelling if more than one virus family was analyzed and compared. Furthermore, can this analysis be extended to estimate the timeline of virus evolution deeper, beyond the family level? Hopefully, at least, this will be addressed in future work. Perhaps, worth mentioning in the Discussion. ********** 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 Reviewer #2: Yes: Eugene V Koonin 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.. 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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 %TITLE% Ghafari, We are pleased to inform you that your manuscript 'Revisiting the origins of the Sobemovirus genus: a case for ancient origins of plant viruses' 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, Peter D. Nagy Academic Editor PLOS Pathogens Savithramma Dinesh-Kumar 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 Dr Ghafari, We are delighted to inform you that your manuscript, "Revisiting the origins of the <i>Sobemovirus<i> genus: a case for ancient origins of plant viruses," 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, Michael Malim Editor-in-Chief PLOS Pathogens |
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