Peer Review History

Original SubmissionAugust 22, 2020
Decision Letter - Susanna Kar Pui Lau, Editor

Dear Dr Chan,

Thank you very much for submitting your manuscript "SARS-CoV-2 lineage B.6 is the major contributor to transmission in Malaysia" 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.

Your manuscript has been reviewed by three experts in the field. Reviewers have made some major suggestions for improvement. Please address all comments from all reviewers. In particular, you are strongly advised to perform in depth analyses of other genomic regions of the SARS-CoV-2 from different lineages and highlight the importance of this study towards the pandemic as suggested by reviewers.

I am willing to consider your revised manuscript that addresses all the suggestions and criticisms of the reviewer. The modified version of your paper may be sent back to the original reviewers prior to its possible acceptance. We cannot, of course, promise publication at that time.

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,

Susanna Kar Pui Lau, M.D.

Deputy Editor

PLOS Neglected Tropical Diseases

Susanna Kar Pui Lau

Deputy Editor

PLOS Neglected Tropical Diseases

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

Your manuscript has been reviewed by three experts in the field. Reviewers have made some major suggestions for improvement. Please address all comments from all reviewers. In particular, you are strongly advised to perform in depth analyses of other genomic regions of the SARS-CoV-2 from different lineages and highlight the importance of this study towards the pandemic as suggested by reviewers.

I am willing to consider your revised manuscript that addresses all the suggestions and criticisms of the reviewer. The modified version of your paper may be sent back to the original reviewers prior to its possible acceptance. We cannot, of course, promise publication at that time.

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: It is a SARS-CoV-2 retrospective genomic epidemiological study and the authors appear to have taken necessary steps to elucidate their findings as such.

Some clarification/changes regarding the sample sizes is required.

Reviewer #2: The objective of the study is clearly presented, the study design is appropriate, the population has been described. However, the sample size is limited compared to the confirmed cases. There are no ethical concerns. No particular statistics analysis have been used.

Reviewer #3: -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?

Yes

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

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: The results require some clarification/changes. There are no major errors in the analysis.

Reviewer #2: The analysis matches the plan. The results are missing some information and also a new schematic chart would be helpful to better understand where the mutations are located.

Reviewer #3: YES

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

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: The conclusions need some clarification/changes and there is acknowledgement of the limitations of the sequencing studies.

Reviewer #2: No limitations are mentioned. The conclusions reflect the data. However, the authors should highlight the importance of this data in the pandemic, how these data advance the global understanding of SARS-CoV-2 mechanisms of infections, spreading and lethality.

Reviewer #3: YES

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

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: A new schematic chart would be helpful to better understand where the mutations are located.

With this new chart specific for the mutations, the current trees should be changed.

Reviewer #3: NONE

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

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 authors describe a SARS-CoV-2 genomic epidemiology study that took place in Malaysia and the finding of a specific viral lineage that is circulating in SEA regions.

They also find that a certain mutation leads to reduced sensitivity in commercial assays for the virus.

Thanks to the authors to provide all necessary details to gauge the sequencing and analysis protocols used in the study.

It would be very helpful if the significance of the study to researchers and clinicians/diagnostics can be described in greater detail (Abstract and Introduction).

"In particular, we were interested in determining the role of the Tablighi Jamaat gathering in regional spread."

Were the 58 patients from the religious gathering?

In the Methodology, explicit details are needed on how many of the 58 patients were from the religious gathering in Malaysia.

And how many of the other 50 Malaysian sequences were from the religious gathering? (Is it 39?)

The total number of B.6 sequences is not consistent between the last paragraph of Methodology and 3rd paragraph of Results.

A detailed split of B.6 sequences can be provided as: sequenced at UMMC + sequenced at other centers in Malaysia + sequenced at other global centers.

Regarding the events that took place and the statement, "of other Malaysian sequences in GISAID dating from the Tablighi Jamaat gathering".

In the above statement, the timeline of events are not clear.

Also, in the recently published work of the authors "Complete Genome Sequences of SARS-CoV-2 Strains Detected in Malaysia",

Fig. 1A the religious event is dated as 29 Feb - 3 Mar, but in the current study the date is 27 Feb - 1 Mar.

Thus, the authors should describe with detail and certainty about the events that took place and that the sequences were from infections originating at the religious gathering.

Rearranging some final sections of the Methodology and beginning of Results could be helpful.

Fig.1: If there are 39 sequences from the religious gathering why are only 3 highlighted?

To avoid blocking the dendrogram, moving the "red point" to the right side of the sequences would be better.

Fig. 3A: Onlyan outline of the histogram could be sufficient. This would also make the lineage markers more clear to see.

Fig. 3C: Would be helpful to include legend in the figure for Southeast Asian country bars vs other country bars

Reviewer #2: The manuscript “SARS-CoV-2 lineage B.6 is the major contributor to transmission in Malaysia” describes the predominant spreading of the B.6 lineage in Malaysia after a religious mass gathering in Kuala Lumpur. This event is associated with the main wave of COVID-19 cases in Malaysia. The authors analyzed 58 genomes sequences from COVID-19 patients that attended the religious event in Kuala Lumpur and 50 Malaysian sequences available in the GISAID database. The authors detected 9 different lineages, and among these, the B.6 became the predominant cause of community transmission in Malaysia after the likely introduction during the religious mass gathering.

The references are appropriate.

Major revisions:

- The authors use sometimes SARS-CoV-2 and COVID-19 as synonymous. They are not: SARS-CoV-2 is the novel coronavirus, while COVID-19 includes all the medical conditions caused by SARS-CoV-2 (as also correctly stated by the authors in the introduction). I would suggest the authors to review the manuscript and use the correct terminology.

- The authors should consider adding a more in-depth analysis of the sequences and their mutations. The authors just mentioned a mutation in ORF3a, one in the spike protein, and few more. What about the other viral genes? For example, the one in the polymerase mentioned by Pachetti et al, J Transl Med 18, 179 (2020)?

- A schematic chart would be helpful to better understand where the mutations are located.

- A few typos need to be corrected by the authors.

Reviewer #3: This is a well written manuscript demonstrating how genetic analysis can inform about transmission dynamics of SARS-CoV-2.

The study shows very nicely how a religious gathering fuelled the spread of the B.6 lineage in Malaysia. The results are clearly presented and my only comment to the results section is Fig. 3A where I would prefer to see the results as rates for instance per 100 000 population and not actual number of cases.

In the discussion I wonder if the authors could elaborate on whether the B.6 had a higher or lower mortality compared to other lineages?

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

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

Reviewer #3: 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, 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 see https://journals.plos.org/plosntds/s/submission-guidelines#loc-methods

Revision 1

Attachments
Attachment
Submitted filename: Response to reviewer.pdf
Decision Letter - Susanna Kar Pui Lau, Editor

Dear Dr Chan,

We are pleased to inform you that your manuscript 'SARS-CoV-2 lineage B.6 is the major contributor to transmission in Malaysia' 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,

Susanna Kar Pui Lau, M.D.

Deputy Editor

PLOS Neglected Tropical Diseases

Susanna Kar Pui Lau

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: This is a revised manuscript.

Reviewer #2: The authors updated the numbers and figures based on the data available up to September 20th 2020. The authors have taken the necessary steps to describe their findings.

There are no ethical concerns.

**********

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 have been better clarified. Table S3 has been added.

There are no major errors in the analysis.

**********

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 have been improved and clarified.

**********

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 authors have addressed all the comments sufficiently.

Reviewer #2: The authors provided more details regarding the samples and the results.

A more in deep analysis of the sequences has been conducted.

minor revisions:

- the legends for figure 1-2-3 are missing.

**********

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

Formally Accepted
Acceptance Letter - Susanna Kar Pui Lau, Editor

Dear Dr Chan,

We are delighted to inform you that your manuscript, "SARS-CoV-2 lineage B.6 is the major contributor to early pandemic transmission in Malaysia," has been formally accepted for publication in PLOS Neglected Tropical Diseases.

We have now passed your article onto the PLOS Production Department who will complete the rest of the publication process. All authors will receive a confirmation email upon publication.

The corresponding author will soon be receiving a typeset proof for review, to ensure errors have not been introduced during production. Please review the PDF proof of your manuscript carefully, as this is the last chance to correct any scientific or type-setting errors. Please note that major changes, or those which affect the scientific understanding of the work, will likely cause delays to the publication date of your manuscript. Note: Proofs for Front Matter articles (Editorial, Viewpoint, Symposium, Review, etc...) are generated on a different schedule and may not be made available as quickly.

Soon after your final files are uploaded, the early version of your manuscript will be published online unless you opted out of this process. The date of the early version will be your article's publication date. The final article will be published to the same URL, and all versions of the paper will be accessible to readers.

Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Neglected Tropical Diseases.

Best regards,

Shaden Kamhawi

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

Paul Brindley

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .