PGPH-D-23-01866

SARS-CoV-2 Co-detection with Influenza and Human Respiratory Syncytial Virus in Ethiopia: Findings from the severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance, January 01, 2021, to June 30, 2022

PLOS Global Public Health

Dear Dr. Berkessa,

Thank you for submitting your manuscript to PLOS Global Public Health. After careful consideration, we feel that it has merit but does not fully meet PLOS Global Public Health’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.

Please submit your revised manuscript by Jan 05 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at globalpubhealth@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pgph/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

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

Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

We look forward to receiving your revised manuscript.

Kind regards,

Martha I. Nelson

Academic Editor

PLOS Global Public Health

Journal Requirements:

1. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed:

https://www.frontiersin.org/articles/10.3389/fmed.2021.681469/full

https://bmjopen.bmj.com/content/11/11/e053768.full

https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-020-4827-0

In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed.

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.

Additional Editor Comments (if provided):

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

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does this manuscript meet PLOS Global Public Health’s publication criteria? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: N/A

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. 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: No

Reviewer #2: No

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

PLOS Global Public Health 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

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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 study offers valuable insights into the co-detection of SARS-CoV-2 with other respiratory viruses. The exploration of age-related patterns and the call for additional research on pathogenic impacts add depth to the findings. Here are comments that may help improve the paper:

Comments:

•Ensure consistency in terminology; for instance, the manuscript refers to “SARS-COV-2” and “SARS-CoV-2”; choose one consistent term throughout.

•The abstract is well structured, although some refinements in language precision and consistency would enhance its clarity.

•In line 100-101 there is a typographical error “real-time PCR”.

•In line 87-89, please provide specific data or references, such as the rate of co-infections.

•Consider briefly acknowledging key findings or trends from studies conducted in other parts of the world.

•Mention the significance of the study within the Ethiopian context. How will the findings contribute to addressing the local challenges, especially in comparison to studies conducted elsewhere?

•Consider providing a brief rationale for choosing specific variable in the regression analysis, which would enhance the understanding.

•The shift in age categories between Table 1-2 and Table 3 raises a notable point. While Table 2 provides a detailed breakdown of age groups, the transition in Table 3 to broader categories may impact the precision of age-related findings. A transparent explanation of the rationale behind the change in categorization would strengthen the interpretation of age-related associations in the study.

•In line 192, most likely this is likely a typographical error in the sentence “under two age category10”.

•In the multivariable analysis, the number of “yes” cases are relatively low compared to the “no” cases, raising considerations about the stability and precision of the estimated parameters. With this substantial imbalance in the number of cases between groups, there is a risk of limited statistical power, which may affect the reliability of the results and increase the potential for type II errors. The author might explore alternative methods or approaches to mitigate the impact of imbalanced groups in the analysis.

•Add a supplementary table to support the reported overall co-detection proportion (1.3%)

•In line 207, there is an extra comma 0.9%

•In line 208, what was the percentage for India?

•For a more comprehensive context, it would be beneficial for the authors to include the total number of inpatients and outpatients in the study.

Reviewer #2: Could you show any plots of SARI/ILI/SARS-CoV-2/influenza/RSV circulation over time? Was there a time period when the epidemics overlapped and coinfection was more common? What was the seasonality of these infections over this 18-month time period? Did SARS-CoV-2 alter the expected seasonal timing of influenza or RSV? Was there a larger flu or RSV epidemic than usual, like there was in Western countries where lockdowns meant no flu or RSV activity for much of 2020-2021? Did these viruses rise and fall at the same time across all 14 sites?

It would be nice to have a map of the location of the study sites, shaded by population density or annotated with major cities.

The methods say that the assay distinguishes influenza A and influenza B. Was there enough power to compare flu A and B?

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6. 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.

Do you want your identity to be public for this peer review? If you choose “no”, your identity will remain anonymous but your review may still be made public.

For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

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[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.]

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SARS-CoV-2 Co-detection with Influenza and Human Respiratory Syncytial Virus in Ethiopia: Findings from the severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance, January 01, 2021, to June 30, 2022

PGPH-D-23-01866R1

Dear Mr. Berkessa,

We are pleased to inform you that your manuscript 'SARS-CoV-2 Co-detection with Influenza and Human Respiratory Syncytial Virus in Ethiopia: Findings from the severe acute respiratory illness (SARI) and influenza-like illness (ILI) sentinel surveillance, January 01, 2021, to June 30, 2022' has been provisionally accepted for publication in PLOS Global Public Health.

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.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they'll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact globalpubhealth@plos.org.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Global Public Health.

Best regards,

Martha I. Nelson

Academic Editor

PLOS Global Public Health

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Your paper has been accepted for publication at PLOS Global Public Health. In the future, if you could please format your response to reviewer comments a little differently, it would speed the second review process and save everyone time. By this I mean include quoted text and line numbers in each response, so the reviewer can easily cross reference the response back to the revised manuscript. For example:

Reviewer Comment: Please do X.

Author Response: We have done X in lines 100-121 of the revised manuscript, see quoted text below.

["New text from lines 100-121."]

Otherwise it takes reviewers a lot of time to sort through all the responses and delays the review process.

Reviewer Comments (if any, and for reference):

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

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2. Does this manuscript meet PLOS Global Public Health’s publication criteria? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. 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: No

Reviewer #2: Yes

**********

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

PLOS Global Public Health 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

**********

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: The manuscript is well-organized and provides a comprehensive analysis of SARS-CoV-2 co-detection with other respiratory viruses in Ethiopia. The authors have addressed all previous comments and suggestions. The introduction sets the context, highlighting the research gap. The methods are detailed, outlining surveillance sites, criteria, and laboratory procedures. Results are clearly presented, covering prevalence rates and associated factors. The discussion interprets findings and suggests future directions. Overall, it's a robust study contributing valuable insights to the field.

Reviewer #2: (No Response)

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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.

Do you want your identity to be public for this peer review? If you choose “no”, your identity will remain anonymous but your review may still be made public.

For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

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