https://orcid.org/0000-0003-3161-4796
Peer Review History
| Original SubmissionAugust 11, 2020 |
|---|
|
PONE-D-20-25162 High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing PLOS ONE Dear Dr. Scaria, 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 find a summary of the reviews appended below. The reviewers recommend reconsideration of your paper following major revision. I invite you to resubmit your manuscript after addressing all reviewer comments. When resubmitting your manuscript, please carefully consider all issues mentioned in the reviewers' comments, outline every change made point by point, and provide suitable rebuttals for any comments not addressed. Please submit your revised manuscript by Dec 04 2020 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. Please include the following items when submitting your revised manuscript:
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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Obul Reddy Bandapalli, MSc, PhD 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. Thank you for including your ethics statement: 'The study was approved by the Institutional Human Ethics Committee (IHEC No. Dated CSIR-IGIB/IHEC/2020-21/01).' a. Please amend your current ethics statement to include the full name of the ethics committee/institutional review board(s) that approved your specific study. b. Once you have amended this/these statement(s) in the Methods section of the manuscript, please add the same text to the “Ethics Statement” field of the submission form (via “Edit Submission”). For additional information about PLOS ONE ethical requirements for human subjects research, please refer to http://journals.plos.org/plosone/s/submission-guidelines#loc-human-subjects-research 3. Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified (a) whether consent was informed and (b) what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). If the need for consent was waived by the ethics committee, please include this information. [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? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Authors has done reasonable and robust approaches for identification of SARSCOV2 using NSG platforms and validated them in few patients. However i have following concerns which need attention by the reviewers and I believe addressing this issue would enhance the validity of the work 1. How we can verify the analysis done at genetic levels with proteins based information. 2. Whether approach actually translate into proteins levels and whether authors identified some of the major antigens which actually bind to the ACE2 receptors. 3. I would advice author to pickup clinical isolate of the covid 19 , infect VeroE6 cells and do the analysis of these major determinant of the virus (ORF) which are responsible not only for the diagnosis but also for the viable infection in host Minor revision Reviewer #2: The manuscript submitted by Bhoyar et al. have used COVIDseq NGS to detect SARS-CoV-2, found new variants and performed a phylogenetic variation. It is a good study with information on evolution of SARS-CoV-2, which can be used in the subsequent studies to understand the impact of specific mutations. Given the ongoing pandemic, I consider that the study is of high significance. However, I have listed some comments for the authors to address. 1. The authors claim that this method can be used as a confirmatory test and a potential high sensitivity assay for detection of SARS-CoV-2. Also, they mention in their discussion that “COVIDseq test ourpeformed with increased sensitivity, precision and accuracy compared to RT-PCR”. I agree that it can be used as a large-scale rapid detection method/confirmatory test but I have a concern regarding their claim with respect to its sensitivity/precision/accuracy compared to RT-PCR, based on the data given in Supplementary Table 4a. I see that 16/655 RT-PCR positive positive samples were not detected in comparison to detecting the viral RNA in 6/655 RT-PCR negative samples. Similarly, 25/43 Pan-Sarbeco positive samples were not detected by their method. It would be helpful if authors can address this concern and discuss/state accordingly in their manuscript. Will it be fair to say that this method has comparable sensitivity with RT-PCR? Also, it would be helpful if authors can discuss the possible technical reasons for discrepancy between the tests. 2. I am wondering if the authors can comment on the geographical distribution/chronology of the samples they analyzed and the genetic variants of the SATS-CoV-2, they detected. Also, it might be helpful if they can elaborate in their discussion on phylogenetic clades them mention about. They are named so first time or they are using clades name based on previous studies? It is not clear. It will also be helpful if they can include in their discussion what the new clades/mutation rates mean for the pandemic in India. 3. For the benefit of readers from diverse background a brief description on pan-sarbeco testing should be included. 4. The authors mention that 4 different RNA extraction methods were used for preparing cDNA. It is not clear if they combined RNA from these methods or carried out testing separately. Clarification would be helpful. 5. A suggestion for future consideration: I am wondering if authors are losing some RNA during phenol-chloroform purification after DNAse treatment. Would it worth exploring TURBO kit to remove the DNAse, which does not involve additional purification step like phenol-choloroform method. Minor editing needed: - Line 74-75 “this approach will become more effective….”. May be it is a good idea to say “is expected to become more effective…” - In several places hyphen is missing. E.g. line 79 it should be nucleic acid-based and sequencing-based. Address the same throughout the manuscript where hyphen is missing. - Where non-standard abbreviations appear first in the manuscript, should be expanded. E.g. line 119 CPC HT. Please address the same throughout the manuscript. ********** 6. 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 [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.] 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. |
| Revision 1 |
|
High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing PONE-D-20-25162R1 Dear Dr. Scaria, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. 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, Obul Reddy Bandapalli, MSc, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Authors has addressed all of my concerns , the manuscript may be acceptable for the publication after grammatical checks Reviewer #2: (No Response) ********** 7. 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 |
| Formally Accepted |
|
PONE-D-20-25162R1 High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing Dear Dr. Scaria: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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. If we can help with anything else, please email us at plosone@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. Obul Reddy Bandapalli 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 .