Dear Dr. Giovanetti,

Thank you very much for submitting your manuscript "Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil" for consideration at PLOS Neglected Tropical Diseases. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation.

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. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Colleen B Jonsson, PhD

Associate Editor

PLOS Neglected Tropical Diseases

Emma Wise

Deputy Editor

PLOS Neglected Tropical Diseases

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Reviewer's Responses to Questions

Key Review Criteria Required for Acceptance?

As you describe the new analyses required for acceptance, please consider the following:

Methods

-Are the objectives of the study clearly articulated with a clear testable hypothesis stated?

-Is the study design appropriate to address the stated objectives?

-Is the population clearly described and appropriate for the hypothesis being tested?

-Is the sample size sufficient to ensure adequate power to address the hypothesis being tested?

-Were correct statistical analysis used to support conclusions?

-Are there concerns about ethical or regulatory requirements being met?

Reviewer #1: (No Response)

Reviewer #2: na

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Results

-Does the analysis presented match the analysis plan?

-Are the results clearly and completely presented?

-Are the figures (Tables, Images) of sufficient quality for clarity?

Reviewer #1: (No Response)

Reviewer #2: The data is clearly presented

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Conclusions

-Are the conclusions supported by the data presented?

-Are the limitations of analysis clearly described?

-Do the authors discuss how these data can be helpful to advance our understanding of the topic under study?

-Is public health relevance addressed?

Reviewer #1: (No Response)

Reviewer #2: (No Response)

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Editorial and Data Presentation Modifications?

Use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. If the only modifications needed are minor and/or editorial, you may wish to recommend “Minor Revision” or “Accept”.

Reviewer #1: (No Response)

Reviewer #2: The manuscript “Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil” provides a brief report resulting from the analyses of 11 viral genomes. While the dataset is limited, it comes from an epidemiologically interesting region at an important time in the dispersal of the P.1 variant. As such, the manuscript provides information that will be of general interest. The message is simple and clearly presented by the authors. Some minor comments for the authors consideration follow.

1. Ln 78. The authors state that eleven suspected P1 infections resulted from the massive screening program. It is a little unclear exactly what this means. Were only 11 positive samples detected through this screening (I suspect this is not what is meant)? It might be clearer if the number of tests conducted and the number of positive PCR tests were provided. If more than 11 samples were positive, how were these particular samples selected?

2. Ln 129. What was the rationale for using two PCR assays on each sample?

3. Ln 136. Did all four family members travel, or was there evidence of within household spread?

4. It would be of interest to know the spectrum of disease experienced by these individuals.

Editorial suggestions

1. Ln 133. “generated where assigned” should be “generated were assigned”

2. Ln 135. “recently record travel” should be “recently recorded travel”

3. Ln 136. “back into the” should be “back to the”

4. Ln 136-137. “and the other others had” should be “and the others had”

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Summary and General Comments

Use this section to provide overall comments, discuss strengths/weaknesses of the study, novelty, significance, general execution and scholarship. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. If requesting major revision, please articulate the new experiments that are needed.

Reviewer #1: Tosta et.al. present the manuscript entitled “Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil” described a pilot study in the northern region of brazil to recover the 11 SARS-COV2 genomes contain P.1 variant, which is of the active public health concern strain. As P1 variants is the important for public health on the active COVID19 pandemic right now, the manuscript will be interested in researchers of the closely related filed. However, the manuscript needs to be improved, especially in the method section. The inconsistency between method and result needs to be clarified.

Comments

1. The P.1 variant need to be defined in detail at first in the Author summary section.

2. Please provide version of the software used in the study: Guppy, qcat, MAFFT, IQ_TREE

3. As Phylogenetic tree analysis is very important result of the study, I recommend the author give the reader more details how to construct the tree such as what is the parameter used, what is the evolutionary model used. Boot strapping is highly recommended to perform and report as confident of the tree result.

4. It is very inconsistency in the method and result! The authors mentioned that they use Oxford Nanopore sequencing of PCR product from ARCTIC primer set, but the first paragraph of the result mentioned that Ion torrent sequencer was used. The authors need to clarify experimental procedures in a better detail.

5. Figure 1A need to be improved. The annotation of different clades based on known linages need to be reported on the figure. Readers will not gain any knowledge from the figure without the annotation of leakages. By using “Others” is meaningless. Standard tree file format such as newick format need to be shared as a supplementary for the readers.

6. The label on y-axis of Figure 1D is missing.

7. Raw sequence data need to be deposited and shared for the research community in a public database such as NCBI SRA database.

8. For reproducible and transparency of the result, I recommended the authors share the computational notebook or chunk of code used in the study.

Reviewer #2: (No Response)

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Reviewer #1: No

Reviewer #2: Yes: Richard J Webby

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 see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

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. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Dear Dr. Giovanetti,

We are pleased to inform you that your manuscript 'Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil' has been provisionally accepted for publication in PLOS Neglected Tropical Diseases.

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 Neglected Tropical Diseases.

Best regards,

Colleen B Jonsson, PhD

Associate Editor

PLOS Neglected Tropical Diseases

Emma Wise

Deputy Editor

PLOS Neglected Tropical Diseases

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

Reviewer's Responses to Questions

Key Review Criteria Required for Acceptance?

As you describe the new analyses required for acceptance, please consider the following:

Methods

-Are the objectives of the study clearly articulated with a clear testable hypothesis stated?

-Is the study design appropriate to address the stated objectives?

-Is the population clearly described and appropriate for the hypothesis being tested?

-Is the sample size sufficient to ensure adequate power to address the hypothesis being tested?

-Were correct statistical analysis used to support conclusions?

-Are there concerns about ethical or regulatory requirements being met?

Reviewer #1: (No Response)

Reviewer #2: my concerns have been addressed

**********

Results

-Does the analysis presented match the analysis plan?

-Are the results clearly and completely presented?

-Are the figures (Tables, Images) of sufficient quality for clarity?

Reviewer #1: (No Response)

Reviewer #2: my concerns have been addressed

**********

Conclusions

-Are the conclusions supported by the data presented?

-Are the limitations of analysis clearly described?

-Do the authors discuss how these data can be helpful to advance our understanding of the topic under study?

-Is public health relevance addressed?

Reviewer #1: (No Response)

Reviewer #2: my concerns have been addressed

**********

Editorial and Data Presentation Modifications?

Use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. If the only modifications needed are minor and/or editorial, you may wish to recommend “Minor Revision” or “Accept”.

Reviewer #1: (No Response)

Reviewer #2: (No Response)

**********

Summary and General Comments

Use this section to provide overall comments, discuss strengths/weaknesses of the study, novelty, significance, general execution and scholarship. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. If requesting major revision, please articulate the new experiments that are needed.

Reviewer #1: The author improved the manuscript and addressed my comments.

Reviewer #2: my concerns have been addressed

**********

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: Richard Webby