https://orcid.org/0000-0001-9859-1678
Peer Review History
| Original SubmissionJune 2, 2025 |
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PPATHOGENS-D-25-01313 High-Fidelity Long-Read Sequencing of an Avian Herpesvirus Reveals Extensive Intrapopulation Diversity in Tandem Repeat Regions PLOS Pathogens Dear Dr.Szpara, Thank you for submitting your manuscript to PLOS Pathogens. After careful consideration, we feel that it has merit but does not fully meet PLOS Pathogens's publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript within 30 days. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plospathogens@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/ppathogens/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: * A rebuttal letter that responds to each point raised by the reviewers (#2 and #3). You should upload this letter as a separate file labeled 'Response to Reviewers'. This file does not need to include responses to any formatting updates and technical items listed in the 'Journal Requirements' section below. * A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. * An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, competing interests statement, or data availability statement, please make these updates within the submission form at the time of resubmission. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. We look forward to receiving your revised manuscript. Kind regards, Deepak Shukla Academic Editor PLOS Pathogens Robert Kalejta Section Editor PLOS Pathogens Sumita Bhaduri-McIntosh Editor-in-Chief PLOS Pathogens orcid.org/0000-0003-2946-9497 Michael Malim Editor-in-Chief PLOS Pathogens orcid.org/0000-0002-7699-2064 Journal Requirements: 1) Please ensure that the CRediT author contributions listed for every co-author are completed accurately and in full. At this stage, the following Authors/Authors require contributions: Alejandro Ortigas-Vasquez, Christopher D Bowen, Daniel W Renner, Susan J Baigent, Yaoyao Zhang, Yongxiu Yao, Venugopal Nair, David A Kennedy, and Moriah L Szpara. Please ensure that the full contributions of each author are acknowledged in the "Add/Edit/Remove Authors" section of our submission form. The list of CRediT author contributions may be found here: https://journals.plos.org/plospathogens/s/authorship#loc-author-contributions 2) Please provide an Author Summary. This should appear in your manuscript between the Abstract (if applicable) and the Introduction, and should be 150-200 words long. The aim should be to make your findings accessible to a wide audience that includes both scientists and non-scientists. Sample summaries can be found on our website under Submission Guidelines: https://journals.plos.org/plospathogens/s/submission-guidelines#loc-parts-of-a-submission 3) Please upload all main figures as separate Figure files in .tif or .eps format. For more information about how to convert and format your figure files please see our guidelines: https://journals.plos.org/plospathogens/s/figures 4) Please upload a copy of Figure S1-S4 which you refer to in your text on pages 12, 15, 19, and 21. Or, if the figure is no longer to be included as part of the submission please remove all reference to it within the text. Reviewers' Comments: 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: The authors have responded appropriately to the issues raised by the reviewers. Reviewer #2: In this revised manuscript titled: High-Fidelity Long-Read Sequencing of an Avian Herpesvirus Reveals Extensive Intrapopulation Diversity in Tandem Repeat Regions, Renner DW. et al. addressed most of the concerns raised by the reviewers in the discussion section. The revision does not have any new data or significant improvement. Overall, this manuscript provided significant detail on the difference within the tandem repeat regions among different strains of MDV. However, it did not highlight the key features of tandem repeats that are unique to different strains. Fig. 1D is not informative about the heterogeneity of tandem repeats between attenuated strains and virulent strains. Fig. 1D could be used to summarize the differences in tandem repeats unique for different strains investigated here. Additionally, the discussion section could include a synthesis section on the various tandem repeats. Are there tandem repeats that could be used to predict the virulence of the virus? What kind of tandem repeats could be seen in attenuated or virulent MDV? What is the driving force for the heterogeneity in the tandem repeats between different strains or within a specific strain? Reviewer #3: The revised manuscript is improved, and the authors addressed my concerns. There are a few minor issues with the revised manuscript. Sentence 532-534, “In addition to observing a wide range of copy numbers (2-37 copies) in CVI988, we found that no length was supported by more than 12% of the reads mapping to either locus.” I find this statement difficult to interpret. Is there a better way of stating this? Sentence 568-570, “Notably, our new model suggests that both of the proline-rich regions found in the MDV genome (i.e., UL36-PRR, Meq- PRR) exhibit complex repetitive patterns that are highly variable across MDV strains.” Please expand on this new model. Perhaps a figure is needed. Proline rich region variations in UL36 and RLORF 7 (meq) have been known for some time. For meq, (please add the following reference): Shamblin CE, Greene N, Arumugaswami V, Dienglewicz RL, Parcells MS. Comparative analysis of Marek's disease virus (MDV) glycoprotein-, lytic antigen pp38- and transformation antigen Meq-encoding genes: association of meq mutations with MDVs of high virulence. Vet Microbiol. 2004 Sep 8;102(3-4):147-67. doi: 10.1016/j.vetmic.2004.06.007. PMID: 15327791. For UL36 (already added) Spatz SJ, Silva RF. Sequence determination of variable regions within the genomes of gallid herpesvirus-2 pathotypes. Arch Virol. 2007;152(9):1665-78. doi: 10.1007/s00705-007-0992-3. Epub 2007 Jun 8. PMID: 17557133. Besides these minor issues, the data is well presented in a well written manuscript with beautiful figures. ********** 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: None. Reviewer #2: No new experiment is requires. Reviewer #3: none ********** 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: Fig 1D should be revised to summarize the differences in tandem repeats unique for different strains investigated here. Reviewer #3: minor issues with their meq and ul36 new model ********** 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 Reviewer #3: No Figure resubmission: 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. Registration is free. 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 PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. If there are other versions of figure files still present in your submission file inventory at resubmission, please replace them with the PACE-processed versions. Reproducibility: To enhance the reproducibility of your results, we recommend that authors of applicable studies 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. 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 |
| Revision 1 |
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Dear Moriah, We are pleased to inform you that your manuscript 'High-Fidelity Long-Read Sequencing of an Avian Herpesvirus Reveals Extensive Intrapopulation Diversity in Tandem Repeat Regions' 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, Deepak Shukla Academic Editor PLOS Pathogens Robert Kalejta Section Editor PLOS Pathogens Sumita Bhaduri-McIntosh Editor-in-Chief PLOS Pathogens orcid.org/0000-0003-2946-9497 Michael Malim Editor-in-Chief PLOS Pathogens orcid.org/0000-0002-7699-2064 *********************************************************** 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, "High-Fidelity Long-Read Sequencing of an Avian Herpesvirus Reveals Extensive Intrapopulation Diversity in Tandem Repeat Regions," 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Sumita Bhaduri-McIntosh Editor-in-Chief PLOS Pathogens orcid.org/0000-0003-2946-9497 Michael Malim Editor-in-Chief PLOS Pathogens orcid.org/0000-0002-7699-2064 |
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