PONE-D-19-25070

Modeling Mayaro and Chikungunya Control Strategies in Rio de Janeiro Outbreaks

PLOS ONE

Dear Dr. Contessoto,

Thank you very much for submitting your manuscript "Modeling Mayaro and Chikungunya Control Strategies in Rio de Janeiro Outbreaks" (#PONE-D-19-25070) for review by PLOS ONE. As with all papers submitted to the journal, your manuscript was fully evaluated by academic editor (myself) and by independent peer reviewers. The reviewers appreciated the attention to an important health topic, but they raised substantial concerns about the paper that must be addressed before this manuscript can be accurately assessed for meeting the PLOS ONE criteria. Therefore, if you feel these issues can be adequately addressed, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. We can’t, of course, promise publication at that time.

We would appreciate receiving your revised manuscript by Dec 22 2019 11:59PM. When you are 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.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Abdallah M. Samy, PhD

Academic Editor

PLOS ONE

Journal Requirements:

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

http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

1. Please note that PLOS ONE has specific guidelines on software sharing (http://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-software) for manuscripts whose main purpose is the description of a new software or software package. In this case, new software must conform to the Open Source Definition (https://opensource.org/docs/osd) and be deposited in an open software archive. Please see http://journals.plos.org/plosone/s/materials-and-software-sharing#loc-depositing-software for more information on depositing your software.

[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: No

Reviewer #2: Yes

**********

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

Reviewer #1: No

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 are presenting a mathematical epidemiology modeling approach to describe outbreaks of Chikungunya in Rio de Janerio, Brazil for the years 2016, 2018, and 2019. Parameters for the Chikungunya model are obtained from the published literature and unknown parameters are estimated using the best fit to the solved equation. Then, parameters for Mayaro virus are plugged in the equation in order to calculate the basic reproduction number for Mayaro in the same geographic region. Finally, for Chikungunya in the year 2018, the authors developed equations resembling three vector control strategies.

The article is well written and their modeling is a book approach to vector-borne disease mathematical modeling. Although well developed, the paper lacks a broader discussion of their findings or lack of them. First, the title of the manuscript is not reflecting what is done in the manuscript, specifically; intervention estimations are done only for Chikungunya in 2018, so Mayaro is never considered apart of the R0 estimation.

Considering the Mayaro model, authors are replacing Chikungunya parameters by those described for Mayaro and then presented results for this pathogen. Although this is valid, the manuscript lacks any other discussion on the topic, this is key in order to consider this manuscript as a scientific contribution worth to be published in a journal, otherwise, we can also fit the parameters for any vector-borne disease (let’s say, Eastern Equine encephalitis, West Nile, etc) and comment on the basic reproduction number. Mayaro specifically grants discussion regarding its life sylvatic/urban life cycle, its endemicity in Latin America (it has been present in the continent longer than Chikungunya), its reservoirs, among others. Further, from the infectious diseases dynamics perspective, is more similar to Yellow fever, thus, the taxonomic justification (Chikungunya and Mayaro are alphaviruses) is short to explain its dynamics in any particular region.

The model is also lacking uncertainty measures. Parameters for the Chikungunya model include ranges for the human and mosquito latent periods. Are the authors using the median of this range? Which are the uncertainties associated with their simulated best-fit distribution of cases presented in Fig 1? Which are the most sensitive parameters in their model? (Sensitivity analysis?)

I believe, the paper could be very useful in a journal considering ‘teaching corners’ since its model implementation is not novel enough but is well explained and developed. It can also be deployed with its code for further teaching applicabilities.

Reviewer #2: It is a well structured paper, clear and easy to read. Authors recognize that models provide insights in the behaviour of epidemics and help further discussions of goverment policies, but do not show real data.

**********

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: Yes: Carolina Ramírez-Santana

[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 be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Modeling Chikungunya Control Strategies and Mayaro Potential Outbreak in the City of Rio de Janeiro

PONE-D-19-25070R1

Dear Dr. Contessoto,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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.

With kind regards,

Abdallah M. Samy, PhD

Academic Editor

PLOS ONE