Dear Dr Nyakarahuka,

Thank you very much for submitting your manuscript "First Laboratory Confirmation and Sequencing of Zaire ebolavirus in Uganda after introduction of cases from the 10th Ebola Outbreak in the Democratic Republic of the Congo, June 2019." 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. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

We apologize for the long delay with your submission. It has taken an unusually long time to secure reviewers. Please attend to the reviewers' requests for minor revisions. Please note the comment about the abstract; it does not meet journal requirements in length (250-300 words) and purpose.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

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

[1] A letter containing a detailed list of your responses to all 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.

Thank you again for your submission to our journal. 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,

Laith Yakob

Associate Editor

PLOS Neglected Tropical Diseases

Andrea Marzi

Deputy Editor

PLOS Neglected Tropical Diseases

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

We apologize for the long delay with your submission. It has taken an unusually long time to secure reviewers. Please attend to the reviewers' requests for minor revisions.

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: The objectives are clearly articulated and the study design is appropriate. The population clearly described and appropriate.

Sample size or statistical analyses do=not apply. Ethical or regulatory requirements were met.

--------------------

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 results are well presented.

--------------------

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: The conclusions are well supported by the data. Limitations are clearly described. The usefulness and public health relevance are adequately discussed.

--------------------

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: The methods section should precise which Elisa kits were used and the Ebola antigen that were used or targetted in the Elisa assays. The validation criteria (cut-off setting) should be explicite as well if the kit is an in-house one. A reference describing the optimisation of the Elisa assays can also be added.

In addition, the method section should mention the place of other investigations (for example the one which led detection of viruses such as CCHF, RVF...) and present the algorithm. Was the Elisa done only for the PCR positive samples?

Reviewer #2: The abstract should be revised for length andclarity.

--------------------

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: This nice paper is brilliantly written and illustrates how complementary are epidemiological investigations and lab testing or sequencing. It also points out the impact of preparedness program and the role of countries collaboration when faciing a commun threat.

Reviewer #2: Nyakarahuka and coworkers have done a terrific job of detailing laboratory confirmation and sequencing of Ebola virus in Uganda after it was introduced from the Democratic Republic of the Congo. The detail of the epidemiology is striking and important work.

This reviewer has only a few suggestions:

1. Please revise the abstract – it is too long for PLOS NTD and misses the guidance to “summarize the most important results with important numerical results given.” Some of these results are summarized nicely in the last paragraph of the paper. It seems important that “the case detected later in August 2019 (201901815) was from a different lineage from the three related cases in June 2019, demonstrating that the two Uganda EVD outbreaks were independent introductions and not the result of ongoing EBOV transmission in Uganda.”

2. With regard to the two independent introductions, it might be more accurate to revise the title of the paper a bit.

3. Apologies, but please revise to confirm to the current nomenclature rules with respect to capitalization and use of italics. Also, species of viruses don’t cause disease, members of species do. The title should probably just say Ebola virus, not the species name.

--------------------

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 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

References

Please 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 rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article's retracted status in the References list and also include a citation and full reference for the retraction notice.

Dear Dr Nyakarahuka,

We are pleased to inform you that your manuscript 'First Laboratory Confirmation and Sequencing of Zaire ebolavirus in Uganda following two independent introductions of cases from the 10th Ebola Outbreak in the Democratic Republic of the Congo, June 2019' 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,

Laith Yakob

Associate Editor

PLOS Neglected Tropical Diseases

Andrea Marzi

Deputy Editor

PLOS Neglected Tropical Diseases

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