Peer Review History
| Original SubmissionFebruary 19, 2024 |
|---|
|
Transfer Alert
This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present.
PONE-D-24-06374Exploring environmental and climate features associated with yellow fever across space and time in the Brazilian Atlantic Forest biomePLOS ONE Dear Dr. Guimarães Kersul, 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.There are mainly clarification of the forest biome definition or side information you did not provided as the mosquitoes density. Please submit your revised manuscript by Jul 20 2024 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 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, Pierre Roques, Ph.D. Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. 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. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 4. Thank you for stating the following financial disclosure: [We are grateful to National Council of Scientific Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq, chamada CNPq/MS-SCTIE-Decit No 22/2019, process number 443215/2019-7) and to the Brazilian Office to Coordinate Improvement of Higher Education Personnel (CAPES) for the fellowship for Maíra G. Kersul from (process number 88887.604207/2021-00)]. Please state what role the funders took in the study. If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."" If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 5. Please include captions for your Supporting Information files (Supporting Information S1 Appendix) at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 6. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments: The 3 reviewers find the work of great interest and quite strong and suggest some minor modifications and clarifications. Most of them should be included in the revision but some request specific answers to the reviewers. [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 Reviewer #3: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: I Don't Know ********** 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 Reviewer #3: No ********** 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 Reviewer #3: 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: Karsul et al. presents a manuscript in which they analyzed data collected from 2016 to 2020 that focused on the occurrence of Yellow Fever (YF) in humans and non-human primates (NHP). A generalized linear mixed regression model was employed to assess the spatial-temporal distribution of YF cases in human and NHP in the Atlantic Forest Biome. The analyses took into account several essential factors, including environmental characteristics, climate factors, vaccinations programs, and the occurrence of YF in at least 2 NHP species, (and perhaps to a much less extent the prevalence of known vector mosquito species in municipal regions). Based on extensive in silico analyses, the data convincingly showed that epizooitic can be correlated to natural forest formation and the presence of the NHP, Calithrix species, and that the epizootics coincided with human cases of YF. The data also revealed several important associations, for example, ~93% of all NHP YF cases occurred with the Atlantic Biome (AB), where these cases peaked in 2017; ~98% of Brazilian human YF cases occurred in 2018 in the AB, not surprising following epizootics; and lower number of cases where vaccination programs were implements. Though the results of the study are largely predictable, considering the occurrence of epizootics, forest expansion and management, and presence/prevalence of mosquito vector species, the extensive statistical analyses provide solid support for these observations. General: 1. Statistical analyses were extensive and convincing 2. Conclusions are well supported. 3. The authors should provide specific references/citations for each of the in silico method used, including online links. 4. Could the authors in include reliable information on the prevalence of the mosquito vector species for humans and NHP in the larger areas surveyed? Are data available to demonstrate specific vector population increases and decreases that correlate to the prevalence of YF in both human and NHP? 5. Substantial editing of the manuscript is required. The Reviewer suggests the authors enlist the assistance and manuscript editing firm to make the appropriate changes. One example of required editing in the first sentence of the ABSTRACT: Line 36-39. "The Atlantic Forest is a biome (AFB) which hosts and favorable conditions for the occurrence of the Yellow Fever virus (YFV) promoted by abundant vectors (Haemagogus and Sabethes species) and several populations susceptible non-human primate (NHP) species (specially Alouatta sp. and Callithrix sp.)." Suggested change: "The Atlantic Forest biome (AFB) provides favorable conditions for the propagation of vector mosquitoes, including Haemagogus and Sabethes species, that disseminate the Yellow Fever virus to both human and non-human primates (NHP), particularly Alouatta sp. and Callithrix sp.)." Reviewer #2: 1. The manuscript titled "Exploring environmental and climatic features associated with yellow fever across space and time in the Brazilian Atlantic Forest biome" presents a study that analyzes the spatiotemporal distribution of yellow fever (YF) cases in humans and non-human primates (NHP) in the Atlantic Forest biome of Brazil between 2016 and 2020. Data collection was based on official records of human cases and epizootics provided by the Brazilian Ministry of Health, encompassing data from Brazilian municipalities within the Atlantic Forest biome with confirmed cases, providing a robust basis for analysis. Although the analyzed data rely on epidemiological surveillance, subject to underreporting and biases in the widely collected information, the authors took these limitations into account in their discussion. Nonetheless, it would be unfeasible to control all variables given the magnitude of the research. 2. For data analysis, a Generalized Linear Mixed Model (GLMM) with a space-time framework was employed to assess the association between dependent variables (presence of epizootics and human prevalence) and a set of independent variables (such as environmental, climatic, vaccination coverage, and presence of NHP species). These models accounted for both fixed and random effects, controlling for time and space. Spatial correlation between municipalities was included in the analysis, conducted using the R software. Results were explored to understand variable behavior patterns in municipalities with and without confirmed disease cases. The authors appropriately opted for logarithmic transformation to normalize data regarding human prevalence. They were also meticulous in selecting independent variables, choosing those with significant correlation with the dependent variable to ensure validity and robustness of results. The use of GLMMs provides a robust approach to analyze the geographic distribution of diseases like yellow fever, controlling for fixed and random effects while incorporating spatial correlation structure. However, availability of more precise data regarding case geolocation could offer a more detailed analysis of spatial distribution patterns of the disease and facilitate better understanding of variable interactions, resulting in deeper insights into the determinants of yellow fever occurrence. While the current approach is suitable with available data, inclusion of more refined data could further strengthen conclusions and guide more precise interventions in combating the disease. 3.The authors provided the data in full in the form of maps, tables, and supplementary data. 4. The research is described clearly, with detailed explanations of the methods. The results are presented in a structured manner, using maps, tables, and supplementary data that facilitate understanding. The conclusions are well-supported by the data presented, making the manuscript suitable for the target audience. The dynamics involved in the circulation of the yellow fever virus are complex and entail the interaction of environmental, climatic, and host factors as described in the study. The research attempts to address various factors but may oversimplify some relationships due to limitations in the data and methods used. It is important to consider that findings may be influenced by other unmeasured factors not accounted for in the analysis, such as the presence of wild and urban vector species, human mobility, and genetic variation of the virus. While the study provides valuable insights, the conclusions should be interpreted with caution. Reviewer #3: Line 104- Maybe include references: da Silva et al, 2010: Hygeia 6(10):77 - 89, Jun/2010 and Couto-Lima et al, 2020: doi: 10.1590/0074-02760200218 Line 118- It is necessary to mention which criteria were used to delimit the Atlantic Forest Biome. Wouldn't official instruments be better, such as Federal Law 11,428/2006 and Decree 6,660/2008? It is possible that any change in this regard could alter the results. Line 145- It is indeed opportune to use a population denominator to weight the cases; Wouldn't the rural population be better? Or maybe test both? Line 149- In addition to presence/absence, in the same way as humans, it wouldn't be interesting to ponder; It is clear that there is no way to use population data on wild primates, but could it not be weighted by the area of the forest environment, which is, after all, the characteristic habitat of these animals? Or perhaps due to the total number of animals reported even without a confirmed laboratory diagnosis (at least there would be a dimension of the number in each municipality)? Lines 151/152- I don't consider this criterion very clear; As I mentioned previously, a possible criterion is what delimits the Atlantic Forest by Decree; or even, studies such as Ribeiro et al., 2009-doi: 10.1016/j.biocon.2009.02.021 or Ribeiro et al., 2011-doi: 10.1007/978-3-642-20992-5_21 Line 177- Interesting: is there any study that led the authors to determine deforestation as an important variable in such a short period? Line 195- I think that the variables related to the two types of climates are very generic; Why did the authors imagine it would be possible to reveal any association? Lines 203- Why not the global vaccination rate? “Descriptive analysis”: I suggest supplementary figures showing the area of vaccine recommendation before 2016, and also vaccination coverage by municipalities before and after the study period. Line 285- In this description of the mathematical formula, the example of the years "2007, 2008,..." confuses the reader; better to put "2016, 2017,...2020". Fig 9- As in figures 3 and 4, it is more enlightening to keep the state boundary lines superimposed on the color gradient of the variable. Why was a heat map drawn up for human cases and not for epizootics? S2 Fig.- Why did they only show the presence of Callithrix and not Alouatta? What exactly would this presence of Callithrix be; would it be the records of deaths and not just those positive for YF? Why is there representation in the maps of forest formation % and Savanna and Grassland (%) beyond the Atlantic Forest Biome polygon while the other descriptors are circumscribed? ********** 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 Reviewer #3: Yes: Luís Filipe Mucci ********** [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 |
|
Exploring environmental and climate features associated with yellow fever across space and time in the Brazilian Atlantic Forest biome PONE-D-24-06374R1 Dear Dr. Guimarães Kersul, 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. If you have any questions relating to publication charges, 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): Thank you for these well detailled and complete answers to the reviewers Reviewers' comments: |
| Formally Accepted |
|
PONE-D-24-06374R1 PLOS ONE Dear Dr. Kersul, 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 If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks 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. 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. Pierre Roques 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 .