PONE-D-20-17377

Association between climate factors and the prevalence dynamics of Japanese Encephalitis

PLOS ONE

Dear Dr. Tu,

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Ram K. Raghavan

Academic Editor

PLOS ONE

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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: Partly

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: I Don't Know

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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

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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

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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: The manuscript titled Association between climate factors and the prevalence dynamics of Japanese Encephalitis incidences (in terms of mosquito density) by Tu et al. presents an approach of nonlinear statistical modeling in predicting the JE dynamics over the region Chongqing (southwest part in China). Author considers the data for the period of 13 years for JE incidences and meteorological par ammeters.

However, the article is written very simply, and I observe not up to the standard of the journal. There are some grammatical issues along lacking the proper definition of study gap.

1. The term climate factor should be replaced with ‘meteorological factor’.

2. The author applies GAM to study the relationship for vector density, and long short term memory model (LSTM) for JE incidence with met. Parameters. No justification for adopting two different modeling aspect.

3. The predictive ability of the model should be written abstract line, and author avoid to do this.

4. The Introduction section is not structured. Globally published literature is missing. The hierarchy should be, global aspect, then continental, then country, then province/district. The author fails to perform this hierarchy. Some

5. Authors wrote, “However, no studies on the prediction of the incidence of JE, which is based on 84 factors such as mosquito density and climate, have been carried out” (pg. 4, line 83-84). In what context the author states this sentence, global or local. Around the globe, researchers have already contributed the stochastic modeling skill for association of JE cases and meteorological parameters (Lin et al., 2012; Pisudde et al., 2017). In what respect the author would like to state that. Justify and clarify.

6. Line #83-88. Is there only the meteorological factors that affect JE vector density for JE incidences? The several other factors like land use land cover changes, built dam, water bodies, socioeconomic status of the exposed population, intervention schemes/policy. Justify, why authors do not take into account, all these?

7. Why author opt for stochastic approach over the deterministic approach, the compartment modeling (deterministic) is also another way to model perfectly. Justification needed.

8. Line #89, instead of Methods, there should be Study Area, Data and Methods. The further subsection may be there.

9. The temporal resolution of data is missing in the ‘Data Collection’ section. For the ease of the scientific community, this should be there. A table may be presented here, for data sources of JE incidences as well as meteorological variables, along with the temporal resolution (daily/weekly/fortnightly/monthly/yearly).

10. The models’ outcome in the result section is not expressed much. The author was only direct to see the tables and figures. The crucial observations are not expressed.

11. The result and methods are very inconsistent. The result outcomes are self-contradictory. The result need to restructure.

12. Discussion is poorly written. Author try to make this very lengthy instead of technical discussion and suggestion. The scientific approach is missing in the discussion part.

13. The conclusion section is missing.

Lin, H., Yang, L., Liu, Q., Wang, T., Hossain, S.R., Ho, S.C., Tian, L., 2012. Time series analysis of Japanese encephalitis and weather in Linyi City, China. Int. J. Public Health 57, 289–296. https://doi.org/10.1007/s00038-011-0236-x

Pisudde, P.M., Kumar, P., Sarthi, P.P., Deshmukh, P.R., 2017. Climatic Determinants of Japanese Encephalitis in Bihar State of India : A Time-Series Poisson Regression Analysis. J. Commun. Dis. 49, 13–18. https://doi.org/10.24321/0019.5138.201729

Reviewer #2: The manuscript presents the results of a correlative analysis between selected climate variables and case incidence of Japanese Encephalitis in central China. The paper addresses a topic that is appropriate for the journal and potentially supplies important information for both basic scientific understanding of environmental influences on disease and for potential application to controlling the disease in this area. The paper compares several methods for deriving correlative models between climate and JE incidence, and does in fact provide the reader with an evaluation of the relative effectiveness of these models. However, the paper paper is frustratingly vague and difficult to follow at times, particularly in its coverage of the basic methodology and in its summary of how the climate variables are related to disease incidence.

The major issue with the paper is that it’s just very difficult to follow exactly what the authors did. Figure 2 shows a flow chart of the methods, showing the sources of data and the general flow of the analysis. It would be helpful to include a table in the body of the paper (rather than the supporting materials) that shows exactly w hat meteorological data are included. There are hints in the paper (temperature extrema seem to be one of the variables) but the reader never really knows for sure, and this becomes a problem later in trying to suss out what the findings of the study really are. All of the data are apparently funneled through the ZIGAM method, but the methods section of the paper never really explains what this is or what it does. It is defined on lines 79-80, and some references are cited. Additionally, in lines 130-141 some additional information is provided. Unfortunately, as a person wholly unfamiliar with this technique, this information was of little use. This may not be the case for readers more familiar with this type of analysis, but for those who are not knowledgeable in this area of analysis, the entire methodology description is not very helpful, at best. Since the entire analysis funnels though this technique, I would strongly urge the authors to write a more complete explanation of what this method does, and why it was chosen for this analysis. Otherwise, the reader is left with the frustrating task of searching through several more papers in order to understand what is in this one.

I had similar issues with the four methods for developing predictive models, LSTM, BPNN, GBM, and SVR. The way the paper is written seems to suggest the LSTM is somehow considered a standard in this type of analysis, and that the other three methods are presented as potentially superior alternatives? Is this correct? IF so, I would suggest that this be made clearer to the reader. On page 7, the paragraph beginning on line 142, some descriptive material for LSTM is provided, but again, in such a way as to be of little help to an unfamiliar reader. I would also note that there is a lot of detail about the other three methods (BPNN, GBM, and SVR) that is simply glossed over. I have only limited experience with neural networks and gradient boosting, but have worked rather extensively with support vector regression, enough to understand that parameter tuning and kernal basis functions are crucial to understanding the effectiveness of them. Absolutely no indication of any of this information is provided. At minimum, one should report the kernal used and the gamma and r parameters. Ideally, the method for determining these parameters should be provided. I suspect that similar information should be provided about the other two methods (GBM, BPNN). Without this type of information, the analysis cannot be replicated, nor does omitting them help other researcher who may wish to use this approach for similar analyses.

In addition to the lack of relevant detail in the methods section, the actual results also lack some specificity. The purpose of the paper was to model the relationship between climate and JE incidence, and to predict the occurrence of cases. Judging from Figure 5, the latter goal was achieved. Unfortunately, it is not really clear how it was achieved. Which climate variables were most relevant, and how relevant were they? Hard to really tell from the body of the manuscript. In the abstract (lines 27-30) it is noted that mean temperature and humidity are important (as is density of mosquito species in livestock sheds, a variable whose provenance is not very clear). In the body of the manuscript, though, this information is very difficult to separate out. Clearly, the authors have developed a method that is potentially useful for predicting JE in this study area, and potentially useful for researchers who may want to understand this disease (and possibly other, similar, mosquito-borne diseases) in other places. Without much clearer elucidation of their methods, this would be difficult to do. One of my “acid tests” for reading a manuscript is, “given similar data, could I repeat their methods, even if I had never used them before.” In this case the answer is no. Even if I were to track down all of the literature cited to support the methods, It’s still not clear how the authors reached their conclusions.

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Reviewer #1: Yes: Dr. Praveen Kumar

Reviewer #2: No

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PONE-D-20-17377R1

Association between meteorological factors and the prevalence dynamics of Japanese Encephalitis

PLOS ONE

Dear Dr. Tu,

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.

Reviewer 1 has raised some minor questions that I think can be addressed very easily.

First of Reviewer 1's comment suggests that you cite a couple of articles. Please know (and it is my recommendation) that you DO NOT have to cite the two articles as these papers do not directly ​inform your work. As far the other comments, please prepare a response and make any changes to the manuscript if you collectively deem necessary.

We appreciate your patience with this review process.

Please submit your revised manuscript by Feb 25 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:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• 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, 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,

Ram K. Raghavan

Academic Editor

PLOS ONE

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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

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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: Partly

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

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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: No

Reviewer #2: Yes

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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

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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: 1. The literature survey still missing the several existing research that have implemented statistical modeling for the association with other Vector Borne Disease like malaria. Author may thoroughly revisit the introduction section and should add some more recent research that focus on Biometeorology. I am suggesting some of the recent findings.

a. Kumar, P., Vatsa, R., Sarthi, P. P., Kumar, M., & Gangare, V. (2020). Modeling an association between malaria cases and climate variables for Keonjhar district of Odisha, India: a Bayesian approach. Journal of Parasitic Diseases. https://doi.org/10.1007/s12639-020-01210-y

b. Kumar, P., Pisudde, P. M., Sarthi, P. P., Sharma, M. P., & Keshri, V. R. (2017). Acute encephalitis syndrome and Japanese Encephalitis, status and trends in Bihar State, India. THE NATIONAL MEDICAL JOURNAL OF INDIA, 30, 317–320. https://doi.org/10.4103/0970-258X.239070

2. How do the meteorological variable play role in the life cycle of JE virus Vector, author should must address here.

3. Do different geography have different threshold for the rainfall, temperature, relative humidity, etc. Author should must discuss in the discussion section.

4. How the build model may be operationalized for public services? Is there any such scope? Brief in short, the application of your model in real time.

5. Author say there is a positive effect on the outbreak with a lag 1-month of some meteorological variable. Is this really feasible, as the mosquito complete the life cycle within a month. A justification should be added.

I would like to see the further changes done by the author.

Reviewer #2: My previous concerns with the paper were that it lacked important details on the data used and the analysis methods. These have now been addressed. There is no further revision needed.

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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: Yes: Praveen Kumar

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.

Association between meteorological factors and the prevalence dynamics of Japanese Encephalitis

PONE-D-20-17377R2

Dear Dr. Tu,

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,

Ram K. Raghavan

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: