Peer Review History
Original SubmissionSeptember 14, 2020 |
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PONE-D-20-28958 Cohort profile: Study on the persistence of Zika virus in body fluids of patients with ZIKV infection in Brazil (ZIKABRA Study) PLOS ONE Dear Dr. Calvet, 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. A large rewritting is requested taking in accoun the general comment from the reviewer 2. As the persistence is the main item analysed here the virology data (ie RNA detection or virus isolation) cannot be partialy skipped as noted by the reviewer 2. The description of the cohort building may be improved by a flowchart as suggested by reviewer 1. Altogether the comments of the 2 reviewers pointed out a paper that deserved to be improved by some clarification in the material and method (and mainly the cohort description) and more carefully linked with the former of future papers that the authors plane to do with this work to improve the discussion conclusion. Please submit your revised manuscript by Nov 23 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, Pierre Roques, 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. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. In your revised cover letter, please address the following prompts: a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially identifying or sensitive patient information) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. Please see http://www.bmj.com/content/340/bmj.c181.long for guidelines on how to de-identify and prepare clinical data for publication. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. We will update your Data Availability statement on your behalf to reflect the information you provide. 3. One of the noted authors is a group or consortium [ZIKABRA Study Team]. In addition to naming the author group, please list the individual authors and affiliations within this group in the acknowledgments section of your manuscript. Please also indicate clearly a lead author for this group along with a contact email address. Additional Editor Comments (if provided): [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: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A 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: No 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: No 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: It is great to see a study of this important health issue in Brazil. This is an important arbovirus in Latin America and elsewhere. However, there are some issues that need to be addressed. Line 89. Screening and recruitment in the cohort: How were the patients recruited? How were the participants referred to the screening locations? Additional details should be provided elaborating upon the information in reference 12. Line 98. Here it is mentioned that no participants were recruited from Rio de Janeiro. Elsewhere the study alludes to recruitment in three cities. As there was no recruitment from Rio de Janeiro, perhaps Rio de Janeiro should not be mentioned in the methods at all. Furthermore, the statement that there was difference in incidence among the cities should be justified by citing a reference. The authors should list the eligibility criteria in greater detail, and provide a list of the inclusion and exclusion criteria. For example, the text suggests that the most important symptom was rash. However, in Table 3, not all participants had rash. ICFs are mentioned on line 107 and line 122. Were there two ICFs? Please clarify. Perhaps a flowchart would make this clearer. Line 116. “the management was done according to regular procedures”. The authors should explain what is meant by “regular procedures”. Line 120. “Individuals with rRT-PCR…”. Was the PCR qualitative or quantitative? If the latter, please list the cycle threshold used to classify a sample as positive. Line 169. The authors repeatedly refer to “Household/sexual contact”. Presumably these two types of contacts are distinct. The study would benefit from clarifying the differences between these two types of contacts. Line 184. Future collaborations. This section of the text is written in the future tense. The previous sections were written in the present tense. It would strengthen the manuscript to reword this text to use the same tense consistently. Line 221. Statistical Analysis. The information about the loss to follow-up after three attempts to contact does not fit in well with the data on statistical methods. This could be moved to the section about Methods: Enrollment. Results Line 261. Currently, the text states that an individual was classified as having prior exposure to malaria if he or she reported malaria in the previous 30 days. This definition may be too restrictive. The definition of the malaria and Yellow Fever could be improved by stating that patients were assessed for recent malaria or Yellow Fever, without limiting the diagnosis to the last 30 days. Line 293. Here it is reported that maculopapular rash was the “most important” symptom. It would make the text more precise if the authors were to list the frequency of rash among the participants, which is given in Table 3. Line 366. Here it is stated that during the recruitment period incidence was low in Brazil. I suggest citing a reference to justify this. Table 2. What is the difference between “Don’t known”, “missing”, and “other”? I suggest replacing “don’t known” with “unknown”. Moreover, it would strengthen the manuscript to list the sample size N and the number of missing. It might benefit the study to compare demographic characteristics of the positive and negative individuals. E.g. was average age different between ZIKV positive and negative individuals? Perhaps the study could mention that the persistence of the virus in sperm is important as it could potentially prolong the persistence of ZIKV in the population. For example, during the Ebola epidemic in West Africa in 2016, the virus was spread both by sexual intercourse as well as by other forms of physical contact. Epidemiological studies demonstrated that the first wave of the epidemic was driven by transmission due to physical contact that was not sexual in nature. Subsequent smaller outbreaks were attributed to sexual transmission. There may be parallels with the transmission of Zika by two different routes: mosquito transmission and sexual intercourse. In connection with this, sexual contacts should be added to the first box of Figure 1. Reviewer #2: Reviewer report- Cohort profile: Study on the persistence of Zika virus in body fluids of patients with ZIKV infection in Brazil Summary Authors of the paper provide a reporting on a cohort that enrolled acute ZIKV patients and their symptomatic and asymptomatic household/sexual contacts. The name of the cohort is ZIKABRA. It is a prospective cohort supported by the WHO and conducted in Brazil to assess the presence and maintenance of ZIKV in human body fluids. Several related markers of infection will be evaluated in the cohort. Overall impression Herein, the authors provide an exhaustive reporting of clinical data of participants enrolled in the ZIKABRA cohort. All models of recording questionnaire frames used in the study are available and the tables contains all results on the clinical status and characteristics of the participants. However, the reporting lacks to developpe specific data and tables about the presence of the virus itself (RNA or virus isolation, as author implement their study especially in places with facilities allowing isolation and detection of the virus). There is only one paragraph, named “Biological specimens”, that shortly summarized the presence of the RNA virus in some fluids. There isn’t any more information instead of the percentage value of positive participants. The authors have already published 2 papers on this cohorts and so they will probably publish paper on each fluid separately, but it should be nice to have more discussion on the results reported in this paper. For example, we haven’t any information of the % of positive male/female for each kind of fluids (obviously apart for semen, breast milk or vaginal secretions). We don’t know neither the positive participants belong to the index case participants or household/sexual contacts, nor the % that correspond to the symptomatic/asymptomatic. Authors noted some information but failed to develop hypothesize about these facts. For instance, they noted that an important part of overweight people in participants, is there any link with disease presentation or the presence of the virus in fluids? Authors issued the potential alternative diagnostic tool due to detection of ZIKV RNA in several fluids in the abstract section but they don’t give more information in the main text about this interesting outcome. Then, authors reported some difficulties to fix the detection of ZIKV RNA, which kind of difficulties to overcome? I invite authors to go little deeper in the analyze of the results presented in this reporting and link these ones with the presence of the virus in body fluids. Minor issues Line 1: The title of the first publication Botto-Menezes et al (doi: 10.3201/eid2505.180904) on this cohort was « Study on the persistence of Zika virus (ZIKV) in body fluids of patients with ZIKV infection in Brazil » and the title of the current submitted paper is : « Cohort profile: Study on the persistence of Zika virus in body fluids of patients with ZIKV infection in Brazil ». Both titles are very closed and it this can be confusing for the reader. May you change the title ? have to be done in results not in discussion. Line 67-68: “… coinfection like dengue…”. Please authors write “dengue and chikungunya” but right next words they use HIV, Hepatitis B (HBV)… If authors describe the virus and not the desease, please correct with “dengue virus (DENV)” and “chikungunya virus (CHIKV)”. Line 85: “… chain reaction (rRT-PCR)…” please homogenized the term for Real Time revers transcription polymerase chain reaction in the text because in line 95 RT-PCR is used. Line 96: used the short form DENV and CHIKV as authors describe viruses (like ZIKV) Line 131: used the short form HBV and HCV as authors mention above for all the virus (Line 68). Line 200: “Specific proposals for collaboration are welcome…”, curious statement in a materiel and methods part. ********** 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 |
PONE-D-20-28958R1 Cohort profile: Study on the persistence of Zika virus in body fluids of patients with ZIKV infection in Brazil (ZIKABRA Study) PLOS ONE Dear Dr. Calvet, 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. You have to stated correctly the objective of the article in both the title and the abstract in order it reflect the result and description you provide. Please submit your revised manuscript by Jan 30 2021 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, Pierre Roques, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (if provided): To have any chance of publication the title and abstract must reflect the contain of the article and thus cannot claimed any virological result (viral load in fluid) that you deleted from the final version. I thus suggest either you provide a true description or you will come back with the data you speach about you would like to provide in a future article. [Note: HTML markup is below. Please do not edit.] 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: (No Response) ********** 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: Partly ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: N/A ********** 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: (No Response) Reviewer #2: Authors answer or/and corrected minor suggestions. However, in the answer to comments, they mentioned that the purpose/objective of this paper was only to report the profile of a cohort and delete any information on viral persistence, submitting results and virologic data to a future publication dedicated to this purpose. They answered only to the minor comments, stayed evasive and avoided the question relative to presence of ZIKV keeping this point for a future publication. I therefore note that this paper is only about the cohort profile but not on ZIKV persistence in body fluid contrary to what the title suggests. ********** 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 [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 2 |
Cohort profile: Study on Zika virus infection in Brazil (ZIKABRA Study) PONE-D-20-28958R2 Dear Dr. Calvet, 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, Pierre Roques, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
Formally Accepted |
PONE-D-20-28958R2 Cohort profile: Study on Zika virus infection in Brazil (ZIKABRA Study) Dear Dr. Calvet: 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. Pierre Roques Academic Editor PLOS ONE |
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