http://orcid.org/0000-0002-3960-0922
Peer Review History
| Original SubmissionMay 18, 2020 |
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Dear Dr. Sato, Thank you very much for submitting your manuscript "A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans" 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 independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments. We would like to note that obtaining reviews from another source can improve the manuscript and facilitate publication but does not entirely satisfy the need for review by independent reviewers chosen by the journal. In this case, we obtained two additional reviews, which are attached. Reviewer 2 felt you had not proven your point and recommended rejection. This seems to us a too severe viewpoint. Reviewer 1, in contrast, noted that you had not effectively responded to the first point made in the reviews you obtained, which clearly stated that experiments using stocks of different viruses to compare infection rates must use stocks normalized based on p24Gag levels measured by ELISA, not by Western blot, which is only semi-quantitative. Therefore, prior to acceptance, all such experiments must be repeated using stocks normalized by ELISA. We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation. When you are ready to resubmit, please upload the following: [1] A letter containing a detailed list of your responses to the 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. Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts. Thank you again for your submission. 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, Bryan R. Cullen Associate Editor PLOS Pathogens Thomas Hope 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'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: Nakano et al show that the lentivirus that passed from chimpanzees to gorillas to establish SIVgor adapted to the APOBEC3G and APOBEC3F genes found in gorillas. The authors map the this change to amino acid changes in Vif . This paper is a nice addition to the literature about how SIVs adapted to new hosts through cross species transmissions via the Vif-APOBEC3 antagonism. The present manuscript was already reviewed (I was not involved in the previous review). The authors have adequately responded to the previous reviewer comments with one exception described below. Reviewer #2: This manuscript reports studies on the mechanism of why SIVcpzPtt Vif does not neutralize gorilla APOBEC3G (gA3G). Because g3G is neutralized by SIVgor Vif, chimeras between SIVcpzPtt and SIVgor Vif proteins were created to map the critical determinant. It was found that this species-specific activity is determined by an amino acid residue at position 16, where SIVcpzPtt and SIVgor Vif proteins have a Met (M16) or Glu (E16) residue, respectively. When a M16E mutation was introduced, SIVcpzPtt Vif became able to neutralize gA3G. Based on this observation, it was concluded that the Vif M16E mutation plays a key role in SIV transmission from chimpanzees to gorillas and then to humans, as described in Title, Abstract, Introduction, and Discussion. However, even though this residue determines SIV Vif activity to neutralize A3G, it does not necessarily mean it has played a role in SIV evolution and cross-species transmission. There is no any evidence provided in this manuscript that supports the central conclusion, which limits its significance of these studies. ********** 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: Major Comments: 1. I am concerned about the authors’ reply to Reviewer #1’s query about whether or not the virus stocks were normalized for p24 before infectivity assays. The authors reply that they were not, but instead point out that Western blots show the same amounts of p24gag. While this may be qualitatively true, much of the data show significance where there is a two-fold difference in infectivity (for example, Figure 4). The standardization of the virus stocks therefore becomes critical to show that variation in virus production does not account for this difference. While the Western blots look about the same, they need to be quantified. This is why most groups routinely standardize their virus stocks through more precise methods (p24 ELISA or RT activity, for example). The authors’ contention that APOBECs and Vif do not affect virus production is not completely true since transfection artifacts of over-expression do lead to changes in virus amounts and that needs to be accounted for. At the least, the authors need to quantify their Western blots and show this data Reviewer #2: 1. A major concern is whether the Vif M16E mutation could occur naturally during SIV evolution. In Fig.2G, a SupT11-CCR5-gA3G cell line was used to propagate SIVcpzPtt. Can the M16E mutation be found in viruses recovered from the cell culture? If not, it would suggest that there are other factors that determine SIV cross-species transmission. 2. In addition to gA3G and gA3F, the activity of gA3D and gA3H should be also determined in order to justify the central role of gA3G in SIVcpzPtt transmission. ********** 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: (No Response) Reviewer #2: In the rebuttal letter, it was shown that unlike the M16E mutation that enables SIVcpzPtt Vif to neutralize gA3G, an E16M mutation did not disable SIVgor Vif from neutralizing gA3G. These results should be included and fully discussed in the manuscript. ********** 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: 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 on PLOS Biology: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5. Reproducibility: To enhance the reproducibility of your results, PLOS recommends that you deposit 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. For instructions see http://journals.plos.org/plospathogens/s/submission-guidelines#loc-materials-and-methods |
| Revision 1 |
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Dear Dr. Sato, We are pleased to inform you that your manuscript 'A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans' 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, Bryan R. Cullen Associate Editor PLOS Pathogens Thomas Hope 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. Sato, We are delighted to inform you that your manuscript, "A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans," 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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