PCOMPBIOL-D-25-00773

Linking multiple serological assays to infer dengue virus infections from paired samples using mixture models

PLOS Computational Biology

Dear Dr. Hamins-Puertolas,

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PLOS Computational Biology

Roger Kouyos

Section Editor

PLOS Computational Biology

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Thank you for submitting your work to PLOS Computational Biology. The reviewers recommended minor revisions -- see their comments attached to this email.

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At this stage, the following Authors/Authors require contributions: Marco Hamins-Puertolas, Darunee Buddhari, Henrik Salje, Angkana T. Huang, Taweewun Hunsawong, Derek A.T. Cummings, Stefan Fernandez, Aaron Farmer, Surachai Kaewhiran, Direk Khampaen, Anon Srikiatkhachorn, Sopon Iamsirithaworn, Adam Waickman, Stephen J. Thomas, Timothy Endy, Alan L. Rothman, Kathryn B. Anderson, and Isabel Rodriguez-Barraquer. Please ensure that the full contributions of each author are acknowledged in the "Add/Edit/Remove Authors" section of our submission form.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Authors:

Please note that one of the reviews is uploaded as an attachment.

Reviewer #1: The review is uploaded as an attachment

Reviewer #2: The authors present a method to jointly analyse multiple serological assays from paired samples. They use mixture models, the application of which is layed out in the manuscript. They show that the use of additional assays improves the accuracy of infection detection. The manuscript is well written, the concepts are well explained, and the approach is well chosen and validated. I only have some minor comments that would help increase the clarity of the manuscript and future use of the methods proposed.

The authors discuss some extensions to their framework, including adding baseline titers and the time since symptom onset as covariates. It would be helpful for future applications if the authors would describe the methodology used in these additional steps more explicitly.

Similarly, the simulation of the synthetic data is performed using the serosim package. It would be helpful if, in addition to the parameter used (table S1) the model used for the generation of the data was given (in main of SM). In particular, it was not clear to me how the immune history was modelled.

Lastly, the model fitting approach is very briefly described. What algorithm was used here? This part would benefit from a bit more details.

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes:  Victoria Cox

Reviewer #2: No

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Attachments

Attachment

Submitted filename: Plos_comp_review_May25.docx

Dear Dr Hamins-Puertolas,

We are pleased to inform you that your manuscript 'Linking multiple serological assays to infer dengue virus infections from paired samples using mixture models' has been provisionally accepted for publication in PLOS Computational Biology.

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Best regards,

Roger Dimitri Kouyos

Section Editor

PLOS Computational Biology

Roger Kouyos

Section Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

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

Reviewer #1: The authors have revised the manuscript based on the suggestions made in the reviews. The clarity around the different models has been improved. The manuscript reads well and as I wrote in the original review, it is interesting and important work. Very minor spot: on line 230 in the tracked changes version, there is a double 'AA'.

Reviewer #2: All comments were well addressed.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: None

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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.

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Reviewer #1: Yes:  Victoria Cox

Reviewer #2: No