PONE-D-20-16036

Clinical impact of respiratory virus in pulmonary exacerbations of children with Cystic Fibrosis

PLOS ONE

Dear Dr. Viviane Mauro Correa Meyer,

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.

Please submit your revised manuscript by September 30, 2020. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're 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.

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). 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'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Abdelwahab Omri, Pharm B, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments:

This is a very simple retrospective analysis of data that I think is flawed in combining static, patient-specific features with variable event-specific features. I would encourage evaluation by a statistician.

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. You indicated that you had ethical approval for your study. In your Methods section, please ensure you have also stated whether you obtained consent from parents or guardians of the minors included in the study or whether the research ethics committee or IRB specifically waived the need for their consent.

3. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions.

In your revised cover letter, please address the following prompts:

a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially identifying or sensitive patient information) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent.

b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. Please see http://www.bmj.com/content/340/bmj.c181.long for guidelines on how to de-identify and prepare clinical data for publication. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories.

We will update your Data Availability statement on your behalf to reflect the information you provide.

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

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: Partly

Reviewer #2: Partly

Reviewer #3: Partly

Reviewer #4: Partly

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: I Don't Know

Reviewer #4: Yes

**********

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: No

Reviewer #2: No

Reviewer #3: Yes

Reviewer #4: Yes

**********

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

Reviewer #4: Yes

**********

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: Although the manuscript is an original work, it is more like an observational study, in which the findings reported are very similar to previously published articles, at least in some form.

The conclusion of this study is very similar to other published reports and thus it does not fulfill the criteria of Replication studies described in the Plos One Guidelines for Reviewers.

I suggest to submit it as an 'Observational study' instead of 'original article'

Reviewer #2: The authors have completed a prospective collection of samples and data on a cohort of subjects with cystic fibrosis. They have determined the viral infection at the time of pulmonary exacerbation and identified factors that differentiate those that are virus positive compared with virus negative.

The authors have provided a comprehensive introduction and discussion with reference to the established literature. They authors have used well established assessment tools in CF research. As such, the study provides some useful information.

I have a few major and minor comments to make that could be addressed by the authors.

Major

1. Since the number of positive subjects is quite limited, I would like to know the power to detect statistical differences between virus positive and negative groups for each outcome. This could be added as an online supplement. I am concerned this study does not have the statistical power to detect differences based on the subject numbers and that is why so few outcomes are significant.

2. If a result is not statistically significant (or even close to p-0.05) then there is no relationship. For example, the authors claim that they virus positive group were younger, but statistically they were not (p=0.3), therefore they are NOT younger. This is described in the results and the discussion. This also includes fever, fatigue antibiotic prescription, P. aeruginosa prevalence, acquisition of P. aeuginosa, intermittent or chronic P. aeruginosa in the whole group or the children <5 years of age (outlined in the discussion).

3. It would be helpful if the authors identified which previous studies mentioned in the discussion (for example: when the authors are discussing the lack of difference in CF severity between virus positive and negative groups) were of a similar age and which were from older children.

Minor

1. Although the article is quite well written and perfectly understandable – the article requires further editing for English.

2. It would be helpful if standard acronyms were used such as URTI (upper respiratory tract illness) instead of URTS.

Reviewer #3: The manuscript by Correa Meyer et al describes an analysis of respiratory virus infection in persons with CF during episodes of pulmonary exacerbation (PE). The aim of the study was to compare virus-positive and virus-negative groups in regards to clinical manifestations, severity of PE and bacterial infection. The authors conclude that prospective studies are needed to assess the impact of viral infection in CF.

A concern with the design and analysis of data in this study is that patient-specific (static) and exacerbation event-specific (variable) characteristics are combined and compared (Table 2). That is, some patient-specific features (eg CFTR genotype, gender pancreatic insufficiency) are counted as independent features for each episode of exacerbation. This seems to introduce confounding. Eg, if an individual heterozygous for F508del had three exacerbation episodes, but by virtue of lack of siblings or age, none of these were associated with viral infection, the three episodes would inflate the number of virus-negative events in the F508del heterozygous group… supporting that viral infection is less common in persons heterozygous for F508del. A more robust multivariable analysis with attention to interactions between variables seems to be required.

On a more minor note: There are implications of causality, when associations are all that can be assessed. Eg: Abstract: do exacerbations cause morbidity in CF … or are these events a sign of morbidity? Eg: Intro: do exacerbations impact disease progression…or are these events a manifestation of lung disease progression? Eg, have the studies cited (refs 3-15) show that viral infection is ‘responsible for’ exacerbation events?

Reviewer #4: This is a study from Brazil in pediatric patients with CF that explores whether viral DNA/RNA can be found during a CF exacerbation. The authors found that 36% of 70 respiratory CF exacerbations were associated with retrieval of viral genetic material from NP swabs.

Comments:

1) Unfortunately this is a relatively small study, and statistical power is quite limited. Therefore the investigators were not able to show significant differences between viral-associated exacerbations and non-viral exacerbations.

2) I think that the study abstract and conclusions need to stress lack of statistical power as a major limitation of this study, this may explain why significant differences between viral-associated exacerbations and non-viral exacerbations was not found.

3) The fact that viral exacerbations were associated with upper resp tract symptoms is of course not surprising, and this may need to be made clearer in the abstract and conclusions.

4) Tables 2 and 5 are far too long and hard to read and all statistical comparisons are non-significant. Please limit these tables to important variables only- please shorten them to 5-6 variables.

5) The discussion should include mention of a study that is highly relevant : Chin M, De Zoysa M, Slinger R, Aaron SD. Acute effects of viral respiratory tract infections on sputum bacterial density during CF pulmonary exacerbations. Journal of Cystic Fibrosis, 14: 482-489, 2015.

**********

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.

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

Reviewer #4: 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.]

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 PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Clinical impact of respiratory virus in pulmonary exacerbations of children with Cystic Fibrosis

PONE-D-20-16036R1

Dear Dr. Viviane Mauro Correa Meyer,

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

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

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 onepress@plos.org.

Kind regards,

Abdelwahab Omri, Pharm B, Ph.D

Academic Editor

PLOS ONE