https://orcid.org/0000-0001-9859-1678
Peer Review History
| Original SubmissionNovember 16, 2021 |
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Dear Dr. Szpara, Thank you very much for submitting your manuscript "Comparison of herpes simplex virus 1 genomic diversity between adult sexual transmission partners with genital infection" 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 two independent reviewers who are experts in the field. Both reviewers found the subject of the study to be significant. Whereas Reviewer 2 was very enthusiastic, Reviewer 1 had major concerns about data analysis and interpretation. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that carefully addresses all of the reviewers' criticisms. In addition, to engage a broader PLOS Pathogens readership, please, restate your major conclusions throughout the manuscript avoiding jargon. 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, Ekaterina E. Heldwein Guest Editor PLOS Pathogens Erik Flemington 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: Both herpes simplex virus 1 and 2 (HSV-1 and HSV-2) can be responsible for genital herpes lesions. HSV-1 classically oral infections and HSv-2 genital infections, however HSV-1 epidemiology is evolving in favour of an increasing number of primary infections occur in the (ana-)genital anatomical niche. Viruses could adapt to their host over time thanks to genetic adaptation. As few data are known for HSV, especially for HSV-1 in the context of genital herpes, all studies concerning this subject are quite interesting. Then, the authors, Rathbun at al., try to study viral genetic diversity in the context of HSV-1 genital herpes. Indeed, they used deep-sequencing analysis to characterize the consensus HSV-1 sequences and to detect minor variants (MVs) within paired sexual partner samples. Reviewer #2: Rathbun et al describe an important and elegant study of genetic variation in herpesvirus genomes among recently infected sexual partners. Both the study and the manuscript are highly accomplished and the authors are to be congratulated. ********** 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: I have read through the manuscript and I have major comments. - To my opinion, the most bothering fault of this study is the analysis of sequencing data. Indeed how is it possible to take into account sequencing data whereas average coverage is very low (see Table 2: e.g. Sample v47_d61-79_gen with 31x of average coverage associated with low viral load of 2.6 cp/mL of virus as data was obtained form 15000 reads with pooled from two replicates or Sample v41_d354_oral with 28x of average coverage associated with low viral load of 2.2 cp/mL of virus as data was obtained form 4100 reads). The use of threshold of 20% supposedly more stringent is not appropriated. To my opinion, to be relevant, only samples with coverage depth <100x should not be considered. Most of the time, low average coverage is associated few reads available and high MV detection: e.g. Sample v47_d61-79_gen with 31x of average coverage associated with 225 MVs or Sample v41_d354_oral with 28x of average coverage associated with 144 MVs. Can we trust that? Moreover, the authors do not discuss quality criteria for sequence trimming in the MM section. May the authors cite publications where these criteria have been used for NGS analysis for HSV genomic diversity estimation? - According to the authors, detection of MVs within the viral population revealed both shared and unique patterns of genetic diversity between partners, and between anatomical niches. But how to make the clear distinction anal and genital niche with self-sampling samples. - Additionally, the authors discuss that genetic drift was detected from spatiotemporally separated samples in as little as three days. This period of time of 3 days appear to be unrealistic. Indeed, even under antiviral selection pressure for instance the evolution pf HSV-1 do not reach such a level of MV within viral genes implicated in antiviral resistance. - It appears there is some discordance between text/tables/figure data makes difficult the interpretation of the study. Either I do not understand or this formulation is not clear enough for well-understanding! I think the authors simplify the tables and the figures to get straight to the point. Reviewer #2: (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: NONE Reviewer #2: There are a number of places where it appears the text is referring to the wrong figure number or sub-number eg 6b rather than 6 C on page 13 line 292. It would be useful for the authors to systematically review all such references for accuracy. The discussion should include comments on the limitations of the methodology in terms of variation in the depth of sequencing coverage between samples and the implications of this on the ability to detect MV. ********** 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, 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. 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| Revision 1 |
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Dear Dr. Szpara, We are pleased to inform you that your manuscript 'Comparison of herpes simplex virus 1 genomic diversity between adult sexual transmission partners with genital infection' 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, Ekaterina E. Heldwein Guest Editor PLOS Pathogens Erik Flemington 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. Szpara, We are delighted to inform you that your manuscript, "Comparison of herpes simplex virus 1 genomic diversity between adult sexual transmission partners with genital infection," 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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