Dear Dr. Vogels,

Thank you for submitting your manuscript entitled "Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus" for consideration as a Research Article by PLOS Biology.

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Paula Jauregui, PhD,

Senior Editor

PLOS Biology

pjaureguionieva@plos.org

Dear Dr. Vogels,

Thank you for your patience while your manuscript "Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus" was peer-reviewed at PLOS Biology. It has now been evaluated by the PLOS Biology editors, an Academic Editor with relevant expertise, and by several independent reviewers.

In light of the reviews, which you will find at the end of this email, we would like to invite you to revise the work to thoroughly address the reviewers' reports.

As you will see below, the reviewers raise some issues that should be addressed before further consideration. We think that the manuscript would benefit of adding more details to explain what context this assay was designed for. The reviewers point to the possibility of cross reactivity with other orthopoxviruses that should be addressed, and their issues regarding the economics of this methodology. Reviewer #1 also highlights the lack of detection of strains or specificity. Please address all the reviewers' issues.

Given the extent of revision needed, we cannot make a decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is likely to be sent for further evaluation by all or a subset of the reviewers.

We expect to receive your revised manuscript within 3 months. Please email us (plosbiology@plos.org) if you have any questions or concerns, or would like to request an extension.

At this stage, your manuscript remains formally under active consideration at our journal; please notify us by email if you do not intend to submit a revision so that we may withdraw it.

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Sincerely,

Paula

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Paula Jauregui, PhD,

Senior Editor

PLOS Biology

pjaureguionieva@plos.org

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REVIEWS:

Reviewer #1: Viral genomics and emerging pathogens.

Reviewer #2: Viral surveillance.

Reviewer #1: The work described in the manuscript "Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus" by Chen et al represents a technical advance in whole genome sequencing amplification of a poxvirus genome using highly multiplexed amplicon-based sequencing. However, its importance is very difficult to assess since the manuscript lacks sufficient evidence that the high coverage achieved with this method actually covers areas of significant variability and phylogenetically informative in the context of the current outbreak. In simple words, it does not matter really if the coverage is high, if it actually does not cover the phylogenetically informative sites.

The authors emphasize that there is an urgent need for a sensitive and broadly applicable sequencing approach, but they do not provide enough data to show that the amplicon-based sequencing approach is sensitive enough to detect the variations that ARE important for understanding the transmission of the virus.

While the amplicon-based sequencing approach described in the manuscript is clearly an improvement over shotgun sequencing for whole genome sequencing of monkeypox virus, there is no evidence presented that shows that the information generated is useful for handling the outbreak. While real-time molecular epidemiology is a revolutionary tool for understanding the transmission of infectious diseases, it is not clear that this approach can be applied to large DNA viruses such as mpox virus in an extremely short timeline. The authors obviously have that information, since their sampling is comprehensive from multiple parts of the world. So, it is somehow strange that the manuscript does not include any evaluation of the diversity described.

Moreover, the authors do not provide any data on the accuracy and reproducibility of the method, which is crucial for evaluating its usefulness for public health surveillance efforts.

Additionally, the authors do not provide evidence of how cross-reactive this system would be with other mpox or orthopoxvirus. Is there a risk that this system is too strain-specific? The authors only discuss this problem in the context of how easy would be to replace/complement the primer set with new additions to fix drop outs. But they do not address how likely this panel would be able to detect other lineage introductions.

One of the key considerations for implementing a strain-specific sequencing system like the one described in the manuscript in low- and middle-income countries (LMICs) or endemic areas of Africa where MPXV is circulating is the availability of resources and infrastructure. While the authors highlight the cost-effectiveness of the amplicon-based sequencing approach, it is important to consider the broader economic and technological landscape of LMICs and endemic areas. In many LMICs and endemic areas, there may be limited resources for public health interventions, let alone advanced molecular sequencing technologies. But, even if the infrastructure were available, it is important to evaluate the return of investment of generating the data.

Whole-genome sequencing is a powerful tool that can provide a detailed understanding of the genomic features of the virus and its transmission dynamics. However, it is also a resource-intensive process that requires significant human and analytical resources. Therefore, it is important to evaluate whether the information generated by whole-genome sequencing of monkeypox virus is worth the investment of resources, especially in the context of limited resources during an outbreak response.

Furthermore, it is important to consider the context-specific nature of the MPXV outbreak. In many cases, outbreaks may be localized and may not require the same level of molecular surveillance as a pandemic situation. In these contexts, the cost-benefit analysis of implementing a strain-specific sequencing system would likely be very different than in a pandemic situation.

Since the authors are presenting their work basically as an enabling technology assessment, all of these components of the cost-benefit analysis should be evaluated and discussed, beyond the actual technical achievement of developing a clearly improved test.

Reviewer #2: This revision looks to establish an economically feasible sequencing approach for MPox during the 2022 outbreak. Kudos for policy translation in the discussion points. I have but minor points.

In the Discussion, it is recommended that periodic long-read metagenomics sequencing be used to identify potential rearrangements in MPox. However, is it possible that something in the amplicon sequencing might trigger this necessity rather than guessing (something like the S gene drop out in SARS-CoV-2)? Else, is the purpose of this method only for infrastructure and economic means? Is it a better move to invest in metagenomics infrastructure and pipelines that are flexible and plug-and-play for pathogens in the future? If so, then some discussion point of equity and LMIC should be made.

Regarding the impact of the manuscript, this is contextual. Is the amplicon coverage supposed to be used for identification and diagnostics or for phylogenetic studies? What is the primary intended utility of this assay?

Further, the issue of cross reactivity with other orthopoxviruses is not addressed and should be addressed at least in the Discussion.

How do the authors propose this method could be used in a fulminant outbreak where mutations are possible? Would a gene drop out be immediately detectable or predicted by this method? How does it compare to current metagenomics identification of mutations?!

Dear Dr. Vogels,

Thank you for your patience while we considered your revised manuscript "Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus" for publication as a Research Article at PLOS Biology. This revised version of your manuscript has been evaluated by the PLOS Biology editors and the Academic Editor.

Based on our Academic Editor's assessment of your revision, we are likely to accept this manuscript for publication, provided you satisfactorily address the following data and other policy-related requests.

1. DATA POLICY:

You may be aware of the PLOS Data Policy, which requires that all data be made available without restriction: http://journals.plos.org/plosbiology/s/data-availability. For more information, please also see this editorial: http://dx.doi.org/10.1371/journal.pbio.1001797

Note that we do not require all raw data. Rather, we ask that all individual quantitative observations that underlie the data summarized in the figures and results of your paper be made available in one of the following forms:

A) Supplementary files (e.g., excel). Please ensure that all data files are uploaded as 'Supporting Information' and are invariably referred to (in the manuscript, figure legends, and the Description field when uploading your files) using the following format verbatim: S1 Data, S2 Data, etc. Multiple panels of a single or even several figures can be included as multiple sheets in one excel file that is saved using exactly the following convention: S1_Data.xlsx (using an underscore).

B) Deposition in a publicly available repository. Please also provide the accession code or a reviewer link so that we may view your data before publication.

Regardless of the method selected, please ensure that you provide the individual numerical values that underlie the summary data displayed in the following figure panels as they are essential for readers to assess your analysis and to reproduce it: Figures 1, 2AB, 3, 4, 6ABCDEFGHIJ and Supplementary figure SF1.

NOTE: the numerical data provided should include all replicates AND the way in which the plotted mean and errors were derived (it should not present only the mean/average values).

Please also ensure that figure legends in your manuscript include information on where the underlying data can be found, and ensure your supplemental data file/s has a legend.

Please ensure that your Data Statement in the submission system accurately describes where your data can be found.

2. I apologize for my previous title suggestion as the name of the disease is not correct. We suggest: "Development of an amplicon-based sequencing approach in response to the global emergence of mpox".

3. Please change to mpox throughout the manuscript when you refer to the disease.

As you address these items, please take this last chance to 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 cover letter that accompanies your revised manuscript.

We expect to receive your revised manuscript within two weeks.

To submit your revision, please go to https://www.editorialmanager.com/pbiology/ and log in as an Author. Click the link labelled 'Submissions Needing Revision' to find your submission record. Your revised submission must include the following:

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*Published Peer Review History*

Please note that 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 see here for more details:

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*Press*

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*Protocols deposition*

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. 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

Please do not hesitate to contact me should you have any questions.

Sincerely,

Paula

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Paula Jauregui, PhD,

Senior Editor,

pjaureguionieva@plos.org,

PLOS Biology

Dear Dr. Vogels,

Thank you for the submission of your revised Research Article "Development of an amplicon-based sequencing approach in response to the global emergence of mpox" for publication in PLOS Biology. On behalf of my colleagues and the Academic Editor, Bill Sugden, I am pleased to say that we can in principle accept your manuscript for publication, provided you address any remaining formatting and reporting issues. These will be detailed in an email you should receive within 2-3 business days from our colleagues in the journal operations team; no action is required from you until then. Please note that we will not be able to formally accept your manuscript and schedule it for publication until you have completed any requested changes.

Please take a minute to log into Editorial Manager at http://www.editorialmanager.com/pbiology/, click the "Update My Information" link at the top of the page, and update your user information to ensure an efficient production process.

PRESS

We frequently collaborate with press offices. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximise its impact. If the press office is planning to promote your findings, we would be grateful if they could coordinate with biologypress@plos.org. If you have previously opted in to the early version process, we ask that you notify us immediately of any press plans so that we may opt out on your behalf.

We also ask that you take this opportunity to read our Embargo Policy regarding the discussion, promotion and media coverage of work that is yet to be published by PLOS. As your manuscript is not yet published, it is bound by the conditions of our Embargo Policy. Please be aware that this policy is in place both to ensure that any press coverage of your article is fully substantiated and to provide a direct link between such coverage and the published work. For full details of our Embargo Policy, please visit http://www.plos.org/about/media-inquiries/embargo-policy/.

Thank you again for choosing PLOS Biology for publication and supporting Open Access publishing. We look forward to publishing your study. 

Sincerely, 

Paula

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Paula Jauregui, PhD,

Senior Editor

PLOS Biology

pjaureguionieva@plos.org