Peer Review History
| Original SubmissionApril 21, 2025 |
|---|
|
Dear Dr. Hossain, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’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 by Dec 14 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Shahina Akter, Ph.D. Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. Please remove all personal information, ensure that the data shared are in accordance with participant consent, and re-upload a fully anonymized data set. Note: spreadsheet columns with personal information must be removed and not hidden as all hidden columns will appear in the published file. Additional guidance on preparing raw data for publication can be found in our Data Policy (https://journals.plos.org/plosone/s/data-availability#loc-human-research-participant-data-and-other-sensitive-data) and in the following article: http://www.bmj.com/content/340/bmj.c181.long. 3. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Additional Editor Comments: Dear Authors, We have reached a decision on your manuscript. While one reviewer recommended rejection without detailed comments, the other reviewers have provided constructive feedback for minor and major revisions. Given the novel premise and overall potential of your work, we invite a major revision. Please address all points raised by Reviewers 2 and 3 in full. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: No Reviewer #2: Yes Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: No Reviewer #2: Yes Reviewer #3: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: No Reviewer #2: Yes Reviewer #3: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** Reviewer #1: Biological experiments should be conducted to develop the vaccine. This is a bioinformatic manuscript for vaccine development (PONE-D-25-20787). The language and writing are fine. However, this manuscript is not of great importance to developing the Cryptosporidium parvum vaccine. Reviewer #2: This is a well written manucript,however some fo the processes in the methodology could be further summerized The The study aim was well stated in lines 148-150 but `` intergrating vaccines`` shouldnt be part of the aim.it fits best inthe introduction section.It would be nice to strucure the abstract,The conclusion as sttted inthe anstract is not apprporroate it should be revised and sated inline withthe study aim. While the Authours have tried to state the conclusion from theor study ,they have also included some discusion of their conclusion.The conclusion shoud revised and clearly stated in line with the study aim and leave out the discussion . Reviewer #3: The study presents a computational design of an mRNA-based multiepitope vaccine targeting Cryptosporidium hominis and C. parvum. While the topic is relevant and aligns with the current trend of using immuno-informatics for vaccine development, the manuscript lacks sufficient methodological rigor, biological validation, and critical interpretation of results. Several sections read like a procedural description rather than a scientific analysis, and there are substantial concerns regarding novelty, clarity, data reproducibility, and presentation. Hence, major revision is strongly recommended before this manuscript can be considered for publication. While the topic is timely and the approach relevant, the manuscript currently lacks methodological rigor, interpretative depth, and structural clarity. The claims of strong immunogenicity and universal coverage are unsupported by robust comparative analysis or experimental evidence. A comprehensive revision with clear validation, data justification, and scientific moderation is required. Major Issues That Must Be Addressed 1. Scientific validation: Add benchmarking or comparison to previously published vaccine constructs or experimental epitopes. 2. Novelty and contribution: Clarify what this study adds beyond existing in-silico works on Cryptosporidium. 3. Data reproducibility: Provide detailed parameters, thresholds, and URLs for all tools, including dataset accession IDs. 4. Figures and tables: Improve quality, labeling, and consistency with captions and in-text references. 5. Discussion: Critically interpret findings and discuss biological limitations of in-silico work. 6. Language: Substantial language polishing and reorganization needed to improve readability. 7. Ethical and data statements: Ensure that the data availability and ethical statements follow journal standards and are placed at the end of the manuscript. My detailed Comments are given as follows 1. Title and Abstract • The title is clear but overly long. Consider shortening to emphasize the main objective (e.g., “In-silico design of a multiepitope mRNA vaccine against Cryptosporidium spp. using reverse vaccinology”). • The abstract is overly descriptive and lacks quantitative insight into why this vaccine design is superior or novel compared to prior in-silico vaccine models for Cryptosporidium. • Statements such as “we firmly endorse ongoing research” are subjective and inappropriate for a scientific abstract. • No validation beyond computational simulation is performed; this limitation should be explicitly stated in the abstract. 2. Introduction • The introduction provides good epidemiological background but is excessively lengthy, with large portions of historical data that distract from the rationale. • The research gap is not sharply defined. The authors should clearly state what previous in-silico vaccine studies exist for Cryptosporidium and what new contribution this work makes (e.g., targeting both C. hominis and C. parvum together). • Many statements lack references to recent literature (e.g., 2023-2025 studies on mRNA vaccine modeling or reverse vaccinology). The following articles are worthy to read and cite. https://doi.org/10.15586/qas.v15i1.1210 https://doi.org/10.1016/j.intimp.2024.113345 https://doi.org/10.1038/s41598-025-98151-4 https://doi.org/10.1038/s41598-025-96989-2 https://doi.org/10.1080/19476337.2023.2296006 https://doi.org/10.1038/s41598-025-00166-4 https://doi.org/10.1007/s12033-025-01477-7 https://doi.org/10.1016/j.intimp.2024.113241 https://doi.org/10.1016/j.intimp.2025.115492 https://doi.org/10.31083/j.fbl2905176 • The transition from epidemiology to computational vaccine design is abrupt. The hypothesis and study objectives should be concisely stated. 3. Materials and Methods • This section is highly procedural and lists tools/servers without methodological justification or parameter explanation. • Critical missing details: o Threshold values used for epitope screening (e.g., VaxiJen score cutoffs). o Criteria for selecting final epitopes among predicted candidates. o Validation of selected proteins’ antigenicity and conservation. o Details on population coverage computation and specific HLA alleles used. o Lack of description of how structural models were verified for quality (no mention of validation metrics besides RMSD and Ramachandran). • No information is provided on control or benchmarking against known vaccine epitopes. • There is no statistical analysis or error quantification — all outputs are descriptive. • The pipeline lacks reproducibility — for instance, figures and tables appear referenced but are not accompanied by clear legends or supporting data. 4. Results • The results are purely descriptive, with minimal interpretation. • Most figures and tables are referred to but not critically discussed. • The claim of “100% global population coverage” is highly unrealistic and likely reflects overfitting due to inclusion of all alleles — needs recalculation and justification. • The docking and simulation results are not compared with any known control peptides or standard vaccines, making their biological significance unclear. • The MMGBSA results are reported without context; the energy values alone cannot confirm strong or weak binding without benchmarking. • The immune simulation results (C-ImmSim) lack comparative baseline; hence, the conclusions on immune protection are speculative. • Figures lack sufficient resolution and labels; color coding (e.g., for linkers and epitopes) is not standardized or scientifically meaningful. 5. Discussion • The discussion mostly repeats results and does not critically analyze limitations or uncertainties in computational predictions. • There is overinterpretation of in-silico results as if they were experimentally validated. • No comparison is made with existing in-silico vaccine designs for other protozoan parasites (e.g., Toxoplasma, Giardia), which could provide important context. • Statements about global applicability, long-term immunity, and biological stability are speculative without in-vitro or in-vivo validation. 6. Conclusion • The conclusion is overly optimistic and unbalanced — it should acknowledge the limitations of computational predictions and the need for experimental verification. • The statement “the vaccine was predicted to be marginal in stimulating immune response” contradicts earlier claims of strong immunogenicity — this needs clarification. 7. Language and Formatting • The manuscript contains numerous grammatical issues, redundant phrases, and inconsistent use of scientific terms. • Citation formatting is inconsistent (e.g., missing brackets, outdated numbering). • Figures and tables are not clearly referenced or formatted according to PLOS ONE style. • The tone should be scientific and neutral remove promotional or conclusive phrases like “firmly endorse ongoing research.” ********** 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: Yes: George Fei Zhang Reviewer #2: No Reviewer #3: No ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. |
| Revision 1 |
|
A novel mRNA-based multiepitope vaccine candidate against Cryptosporidium hominis and Cryptosporidium parvum employing Reverse-Vaccinology and Immunoinformatics approaches PONE-D-25-20787R1 Dear Dr. Imam Hossain, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support . If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Shahina Akter, Ph.D. Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #2: (No Response) Reviewer #3: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #2: Yes Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #2: Yes Reviewer #3: N/A ********** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #2: Yes Reviewer #3: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #2: Yes Reviewer #3: Yes ********** Reviewer #2: The authours have adequately addresed the comments and recommendations by made by the review. i have no concerns Reviewer #3: The manuscript has been comprehensively revised and the authors have answered all the reviewers comments, I would recommend the manuscript for publication. ********** 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 #2: No Reviewer #3: No **********
|
| Formally Accepted |
|
PONE-D-25-20787R1 PLOS One Dear Dr. Hossain, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. 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. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Shahina Akter Academic Editor PLOS One |
Open letter on the publication of peer review reports
PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.
We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.
Learn more at ASAPbio .