PONE-D-19-16505

Genetic evolution of influenza viruses among selected countries in Latin America, 2017–2018

PLOS ONE

Dear Dr Palekar,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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The manuscript has to undergo a language editing with the help of a native speaker and/or editing service. Samples were collected during a limited time period, please add a Discussion point as to how this could have affected the results.

In order to properly interpret the data from this manuscript, a comparison with global genetic diversity of the virus would be necessary.

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We would appreciate receiving your revised manuscript by Oct 25 2019 11:59PM. When you are ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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Peter Gyarmati

Academic Editor

PLOS ONE

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2. Please  change Fig.1, so that the names of the axes are clearly legible.

Additional Editor Comments (if provided):

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: N/A

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3. Have the authors made all data underlying the findings in their manuscript fully available?

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The manuscript analyzed influenza A/H1pdm09, A/H3, B/Victoria and B/Yamagata hemagglutinin sequences from clinical samples from 12 National Influenza Centers in ten countries with a collection date from epidemiologic week (EW) 18, 2017 through EW 43, 2018. These sequences were used for phylogenetic reconstruction. They reported that hemagglutinin sequences from the participating countries were highly concordant with the genetic groups of the influenza vaccine-recommended viruses for influenza A/H1pdm09 and influenza B. Since this study is helpful to allow public health decision makers to make informed decisions about prevention and control strategies, this study is relevant and would deserve publication. On the other hand, the quantity and analysis period of clinical samples and HA sequences of influenza virus is still limited, which influence the reliability of the study to some extent.

Reviewer #2: In this manuscript Juliana and coworkers construct the phylogeny consensus for the influenza virus on the basis of previously sequenced data from the data banks. They have studied the influenza A/H1pdm09, A/H3, B/Victoria and B/Yamagata HA sequences for the year 2017-2018. I think they have to expand the time duration as only for one year it can't be concluded that which specific strain is circulating in the area. In the manuscript there are several English mistakes. It need to read it properly and correct the English mistakes. In line 100 reference style is not correct. Please make sure all the references are correct and in appropriate order and style. Also make the sample numbers very clear it make the reader to confuse about the sample numbers for each specific strain of Influenza virus.

Reviewer #3: See attachment for full comments.

Overview:

The manuscript analyzes influenza virus evolution in Latin America using sequence data in the GISAID database. The authors identify a set of hemagglutinin sequences representing influenza A/H1pdm09, A/H3, and B generated from Latin American sequencing centers and from the US WHO Collaborating Center based on samples collected at Latin American sentinel sites from 2017 to 2018. They perform a phylogenetic analysis of these sequences, identify the substitutions that occur along the phylogeny, and calculate the frequencies of viral clades. They find that sequences from Latin America are broadly aligned with clade frequencies worldwide.

The manuscript addresses the important topic of influenza's genetic diversity in an under-surveilled part of the world. The analyses are appropriately conducted according to standard methods, although the phylogenetic methods themselves are not especially novel. I find that the manuscript could be strengthened by providing more precision about major conclusions regarding the evolution of viruses in Latin American and their clade frequencies relative to other areas of the world. Much of this work can be done through rewriting and clarifying the discussion, but some simple additional analyses would substantially strengthen the manuscript as well.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files to be viewed.]

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Attachments

Attachment

Submitted filename: PLoSOne-Leite-2019-KX.pdf

PONE-D-19-16505R1

Genetic evolution of influenza viruses among selected countries in Latin America, 2017–2018

PLOS ONE

Dear Dr Palekar,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

We would appreciate receiving your revised manuscript by Jan 11 2020 11:59PM. When you are ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

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. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled '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.

We look forward to receiving your revised manuscript.

Kind regards,

Peter Gyarmati

Academic Editor

PLOS ONE

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

Reviewer #3: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: N/A

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: (No Response)

Reviewer #3: The manuscript analyzes influenza virus evolution in Latin America using next-generation sequencing data. In particular, the authors study the extent to which viral genetic diversity in Latin American countries reflects broader, global patterns of genetic diversity. Since the previously submitted version of the manuscript, which I reviewed, the authors have improved the comparison of influenza clade frequencies in Latin America compared to the rest of the world by including a new Figure 7, generated from Nextstrain. I am generally satisfied that the authors have addressed my concerns about presenting a more explicit comparison of regional and global genetic diversity, but the analysis in Figure 7 contains a few remaining oddities that the authors need to correct.

Figure 7 shows global clade frequencies for the four influenza subtypes under study and is derived from the visualization interface at nextstrain.org. It is not clear to me why the y-axes of these plots end at 12% (they should run from 0-100%), or why the diversity of viruses appears to decline after about mid-2018. Both anomalies should be corrected by the authors. For example, the nextstrain.org interface shows that for B/Yamagata, the 172Q clade makes up nearly all viral diversity following 2017, but in Figure 7, the clade appears to decline in frequency until it makes up none of the viral diversity under analysis. It seems likely that the authors set a cutoff date that causes the odd appearance of the graph, but this visualization choice is confusing. It would be better for the authors to present all clade frequencies between 2017 and the present.

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7. 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: Mohsan Ullah

Reviewer #3: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files to be viewed.]

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. Registration is free. 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. Please note that Supporting Information files do not need this step.

Attachments

Attachment

Submitted filename: PLoSOne-Leite-2019-KX-resubmission.docx

Genetic evolution of influenza viruses among selected countries in Latin America, 2017–2018

PONE-D-19-16505R2

Dear Dr. Palekar,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

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With kind regards,

Peter Gyarmati

Academic Editor

PLOS ONE

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