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.

Dear Dr Gandon,

Thank you very much for submitting your manuscript 'Winter is coming: pathogen emergence in seasonal environments' for review by PLOS Computational Biology.  We apologize for the long time of the process and for the un-satisfactory point we have reached. Your manuscript was evaluated by only one referee so far, and the delay was due to a long process of trying to secure at least a second referee. After having invited 13 others, we would like to move forward on the basis of this referee and the evaluation by one of us.

The reviewer indicated the importance of the problem, but raised concerns on the presentation of the arguments and results, and the way the reader would have to construct an understanding of the main idea. We agree with this concern and think that the way the argument is presented may have been itself one reason why we have failed to secure referees (rather than a lack of interest in the subject). 

While your manuscript cannot be accepted in its present form, we are willing to consider a revised version in which the issues raised by the reviewer have been adequately addressed. We believe a clearer version will have a better chance of additional reviews, which we would like to have to make a decision. We cannot promise publication at that time, but we believe this is a more effective course of action than seeking those reviews now. 

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.

Please return the revised version within the next 60 days. If you anticipate any delay in its return, we ask that you let us know the expected resubmission date by email at ploscompbiol@plos.org. Revised manuscripts received beyond 60 days may require evaluation and peer review similar to that applied to newly submitted manuscripts.

In addition, when you are ready to resubmit, please be prepared to provide the following:

(1) A detailed list of your responses to the review comments and the changes you have made in the manuscript. We require a file of this nature before your manuscript is passed back to the editors.

(2) A copy of your manuscript with the changes highlighted (encouraged). We encourage authors, if possible to show clearly where changes have been made to their manuscript e.g. by highlighting text.

(3) A striking still image to accompany your article (optional). If the image is judged to be suitable by the editors, it may be featured on our website and might be chosen as the issue image for that month. These square, high-quality images should be accompanied by a short caption. Please note as well that there should be no copyright restrictions on the use of the image, so that it can be published under the Open-Access license and be subject only to appropriate attribution.

Before you resubmit your manuscript, please consult our Submission Checklist to ensure your manuscript is formatted correctly for PLOS Computational Biology: http://www.ploscompbiol.org/static/checklist.action. Some key points to remember are:

- Figures uploaded separately as TIFF or EPS files (if you wish, your figures may remain in your main manuscript file in addition).

- Supporting Information uploaded as separate files, titled Dataset, Figure, Table, Text, Protocol, Audio, or Video.

- Funding information in the 'Financial Disclosure' box in the online system.

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. 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.

To enhance the reproducibility of your results, we recommend that 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 here. 

We are sorry that we cannot be more positive about your manuscript at this stage, but if you have any concerns or questions, please do not hesitate to contact us.

Sincerely,

Mercedes Pascual

Associate Editor

PLOS Computational Biology

Virginia Pitzer

Deputy Editor

PLOS Computational Biology

A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

[LINK]

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: see attached

**********

Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

**********

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

Attachments

Attachment

Submitted filename: Review_Seasonality.pdf

Dear Dr. Gandon,

Thank you very much for submitting your manuscript "Winter is coming: pathogen emergence in seasonal environments" for consideration at PLOS Computational Biology.

As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by two referees.  The first referee had commented on the previous version of the manuscript and had requested clarifications and changes to make the work more accessible. She/he is now satisfied with the changes and provides minor suggestions. The second referee agrees that the work is a valuable and interesting contribution.  But  his/her major concerns are again with the way the work is presented, in particular the lack of  sufficient context motivating the work and placing its relevance into a more tangible and historical context. Specific suggestions are made for the consideration of a number of studies that would help doing this.  We happen to agree that the manuscript can be written in a way to reach a broader audience and goes from the technical contribution to deeper context and discussion.

In light of this review (below this email) and our own assessment, we would like to invite the resubmission of a revised version that takes into account the reviewer's comments in a way that makes the results of the work more compelling. We cannot make any decision about publication until we have seen the revised manuscript.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to the review comments and a description of the changes you have made in the 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.

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts.

Thank you again for your submission and your patience with the delays in the current circumstances.

We hope you will consider this additional request a constructive attempt to make the manuscript as accessible and appealing as possible to our readers.

Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Mercedes Pascual

Associate Editor

PLOS Computational Biology

Virginia Pitzer

Deputy Editor

PLOS Computational Biology

***********************

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: This is a very carefully worked out and mature work that covers a lot of ground from periodically forced natural systems, to their optimal control. The authors have a detailed knowledge of stochastic systems and branching processes, and this has led to the fruition of a deep analysis from many fronts. I learnt a lot from reading this manuscript.

1) The authors have made significant new contributions to the study of forced seasonal systems and highlighted some new (sometimes subtle) important dynamical behavious.

2) I have checked all the maths in the SI that is relevant to the equations and models discussed in the main text.

Minor comments:

*Authors should mention that Eqns 5&6 are derived in the relevant Appendix.

*Page 5 Eqn.5 Perhaps give the value of R0, and pE in the main text, for Fig.2E and 2F so the reader can see this works.

*Ref missing in Section 2.3 of SI

*Fig.2 The notation p(toT, T) is used in the SI, but I don't think it is given in the main text. (I am referring here to the rescaling of t0)

Reviewer #2: The topic and idea developed in this work is very interesting, and I find it particularly valuable that the authors emphasize the importance of working with probabilities rather than with deterministic quantities such as R0. Although R0 is useful for many purposes, it presents limitations, especially for low-transmission situations, among others.

Although the development of expressions and the study of probabilities for the occurrence of major outbreaks are not new, there is a lack of concrete applications and discussion of different transmission scenarios. This theoretical study investigates how the interaction of seasonality, duration and arrival time of the infection, affects the probability of a major outbreak. In particular, the authors contribute to the formalization of an effect that is somehow intuitive which they call “the winter is coming effect”.

Unfortunately, however, the authors do not better exploit the intuitive and biological aspects of this effect in a way that would be accessible to a broader audience (that would be very interested in this topic). The way the paper is written is quite technical. It would benefit from a deeper connection to particular infectious diseases or actual transmission results, mainly in the introduction and discussion sections. For example, the authors could compare/connect their results with Otero et al. 2010, who studied the probabilities of major dengue outbreaks based on the first infection arrival time to the city of Buenos Aires. Another example that could be discussed in this paper is the study of flu arrival times for different cities in the US and UK by Truscott & Ferguson 2012, as well as the results obtained by Dalziel et al. 2018 also for flu. In addition, I was surprised that the authors did not cite and connect their probabilities’ expressions with those in the papers by Bartlett 1964 and by Lloyd et. al 2007. Both papers discuss the probability of pathogen emergence, in direct and vector transmitted diseases.

In conclusion, I like the idea and I think it is a compelling topic that a broad spectrum of readers of this journal and beyond would be interested in. The writing is too technical and needs deeper motivation and discussion related to empirical and intuitive aspects, including a clearer connection to results in other studies of transmissible diseases.

**********

Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Figure 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. 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.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, PLOS recommends that you deposit 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, please see http://journals.plos.org/compbiol/s/submission-guidelines#loc-materials-and-methods

Dear Dr. Gandon,

We are pleased to inform you that your manuscript 'Winter is coming: pathogen emergence in seasonal environments' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Mercedes Pascual

Associate Editor

PLOS Computational Biology

Virginia Pitzer

Deputy Editor

PLOS Computational Biology

***********************************************************