Identifying the interplay between protective measures and settings on the SARS-CoV-2 transmission using a Bayesian network

Pilar Fuster-Parra; Aina Huguet-Torres; Enrique Castro-Sánchez; Miquel Bennasar-Veny; Aina M. Yañez

doi:10.1371/journal.pone.0307041

Peer Review History

Original SubmissionMay 9, 2024
5 Jun 2024 Decision Letter - Liling Chaw, Editor PONE-D-24-17062Identifying the interplay between protective measures and settings on the SARS-CoV-2 transmission using a Bayesian networkPLOS ONE Dear Dr. Huguet-Torres, 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 Jul 20 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 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. 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If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. 5. 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: Please consider the comments from the reviewers. [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: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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: Yes Reviewer #2: 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: 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: Very nice work, I find the topic and the bayesian network approach really interesting and very well presented. I've just highlighted some minor comments. Abstract Very well written Introduction L.10 - 12 Sentence to be revisited, difficult to follow L.28 - 30 References missing L.43 Additionally, describe -> something is missing here (e.g., we describe / our work describes) Materials and Methods L. 46 Maybe number M&M as 2 and Introduction as 1 (do the same for the next sections - Results, Discussion) L.130-133 - Please check the names of the variables to be consistent in the text L.193-195 Please provide more info what Accuracy, Sensitivity Specificity, ROC Area describe? Results + Discussion Very nicely reported Reviewer #2: A very good piece of work. I liked the way you showed the structure of the variables in terms of the BN construction. I think it is a worthwhile addition to the literature, the way the underlying data is used supports the objectives of the paper well. Cross comparisons with other classifiers are helpful in highlighting the strong applicability of BN to this type of problem. I thought you were also honest and realistic about the limits of contact tracing, as a process and the likelihood of infection from the index case, vs contamination from another source. The presence of the handwashing as a non-causal variable was an excellent way to validate both the resulting model and the process. I felt you could have emphasised this more strongly. One aspect that could have been explored was the variability in masks; i.e. the mask type. I was disappointed that although this information was mentioned there was no further exploration. Other studies have shown the different effectiveness of mask types, as well as the expected leakage for infected persons. The limited effectiveness of certain mask types (surgical vs FFP2/N95) against aerosol transmission in poorly ventilated spaces has been documented elsewhere, perhaps your dataset wasn’t large enough or lacked the necessary details to clearly illustrate this signal. Another point which would have benefited from clarification was the status of education and workplace activities during the period of the study (i.e. restrictions, working from home, school or university closures). I assumed in my review that there were no restrictions/lockdown measures in place for work or education in the study region during the period when the data was collected. ****** 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 ******** [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. 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Revision 1
14 Jun 2024 Author Response Dear Editor-in-Chief, Thank you for the opportunity to submit a revised draft of our manuscript titled "Identifying the interplay between protective measures and settings on the SARS-CoV-2 transmission using a Bayesian network” to PLOSONE. We appreciate the time and effort that you and the reviewers have dedicated to providing valuable feedback to our manuscript. We are grateful to the reviewers for their insightful comments, which have strengthened the manuscript. We have highlighted the changes within the manuscript, and our responses to the reviewers below in blue colour. We uploaded the revised version of the manuscript with tracked changes and a clean version. #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 R: Thank you for the feedback. The manuscript has been reviewed and revised to ensure it meets PLOS ONE's style requirements, including file naming conventions. 2. Please note that funding information should not appear in any section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript. R: Thank you for your guidance regarding the handling of funding information. We have promptly addressed this matter by removing all funding-related text from the manuscript, as per your instruction. 3. Thank you for stating the following financial disclosure: "This study was funded by the Royal College of Nurses from the Balearic Islands (Ref.: 2021-0564). This research was also supported by the Florence Nightingale fellowship program, Royal College of Nurses from the Balearic Islands and the Nursing and Physiotherapy Department, University of the Balearic Islands." Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. R: Thank you for your suggestion. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. We will include this statement in the cover letter of the online submission form. 4. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. R: Thank you for your comment. As you suggested, the data has been made available. 5. 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. R: All references have been reviewed, and no retracted references have been identified. 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 R: Thank you. We appreciate your decision. 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes R: Thank you. We appreciate your decision. 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 R: Thank you. We appreciate your decision. 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: Yes R: Thank you. We appreciate your decision. 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: Very nice work, I find the topic and the bayesian network approach really interesting and very well presented. I've just highlighted some minor comments. Abstract Very well written R: Thank you for your comment. Introduction L.10 - 12 Sentence to be revisited, difficult to follow R: Thank you for your suggestion. The sentence has been modified for improved clarity. The new sentence reads: ‘The measures aimed at mitigating the effects of transmission, such as improving ventilation and minimizing exposure time to infected individuals (13-16), have been identified as essential for controlling community transmission (12,17).’ L.28 - 30 References missing R: Thank you for bringing this to my attention. We apologize for the oversight. We have now added the missing references to the manuscript. L.43 Additionally, describe -> something is missing here (e.g., we describe / our work describes) R: Thank you for detecting this error. We modified the sentence. The new sentence reads: ‘Additionally, we describe the interplay between these prevention measures and the characteristics of exposure settings using a Bayesian network approach with data from a national contact tracing program.’ Materials and Methods L. 46 Maybe number M&M as 2 and Introduction as 1 (do the same for the next sections - Results, Discussion) R: Thank you for your suggestion regarding section numbering. However, upon reviewing the journal guidelines, we have decided to remove section numbering as it does not align with the journal's policies. L.130-133 - Please check the names of the variables to be consistent in the text R: Thank you for the observation. We have checked the names of variables in the text. L.193-195 Please provide more info what Accuracy, Sensitivity Specificity, ROC Area describe? R: Thank you for the suggestion. We have added some information related to these concepts in the text. Results + Discussion Very nicely reported R: Thank you for your comment. Reviewer #2: A very good piece of work. I liked the way you showed the structure of the variables in terms of the BN construction. I think it is a worthwhile addition to the literature, the way the underlying data is used supports the objectives of the paper well. Cross comparisons with other classifiers are helpful in highlighting the strong applicability of BN to this type of problem. I thought you were also honest and realistic about the limits of contact tracing, as a process and the likelihood of infection from the index case, vs contamination from another source. The presence of the handwashing as a non-causal variable was an excellent way to validate both the resulting model and the process. I felt you could have emphasised this more strongly. R: Thank you for your comments. As you rightly pointed out, the inclusion of handwashing, or other variables, with non-causal outcomes has underscored the significance of all other preventive and/or protective measures. We appreciate your observation and the value you have added to the study. One aspect that could have been explored was the variability in masks; i.e. the mask type. I was disappointed that although this information was mentioned there was no further exploration. Other studies have shown the different effectiveness of mask types, as well as the expected leakage for infected persons. The limited effectiveness of certain mask types (surgical vs FFP2/N95) against aerosol transmission in poorly ventilated spaces has been documented elsewhere, perhaps your dataset wasn’t large enough or lacked the necessary details to clearly illustrate this signal. R: We appreciate your observation regarding mask types, and we regret that this aspect was not thoroughly explored in the present article. In a previous publication, based on the same sample, the type of mask did not have significant results once adjusted for other variables. Additionally, most participants reported using surgical masks, as per official guidance at the time, which influenced our decision not to include this factor in the Bayesian network model. In our context, and in the social situations in non-clinical environments, FFP2/NP95 face masks were seldom used. We acknowledge though that including information about the type of marks could have contributed to the body of evidence about mask effectiveness. We will therefore include this aspect in the limitations of this study. The new sentence reads: ‘Another limitation of the study is that the variability in the types of masks used by the participants was not thoroughly analyzed, which could have influenced the results.’ Another point which would have benefited from clarification was the status of education and workplace activities during the period of the study (i.e. restrictions, working from home, school or university closures). I assumed in my review that there were no restrictions/lockdown measures in place for work or education in the study region during the period when the data was collected. R: We appreciate your observation regarding the status of education and workplace activities during the study period. We regret the oversight in not providing a detailed clarification in the methodology section of the article. While there were no restrictions on education or workplace activities during the data collection period, there were limitations in other areas, such as bars and social settings. We acknowledge that this aspect could have been elucidated more comprehensively to ensure a thorough understanding of the study context. It's important to note that this information is covered in detail in another article. Furthermore, to address this concern and enhance the clarity and coherence of our work, we will include a concise explanation of the restrictions applicable at that time in the relevant section of the methodology. This addition will facilitate a better understanding of the environmental conditions in which our study was conducted. The new sentence reads: ‘During the data collection period, Mallorca was under the 2nd to 4th level of COVID-19 public health measures ("Control Situation" and "High Risk"). In the food and hospitality sector (ie, restaurants and bars), up to six people could sit at a table, with social gatherings limited to a maximum of 6 individuals.’ https://doi.org/10.1371/journal.pone.0307041.r002
28 Jun 2024 Decision Letter - Liling Chaw, Editor Identifying the interplay between protective measures and settings on the SARS-CoV-2 transmission using a Bayesian network PONE-D-24-17062R1 Dear Dr. Huguet-Torres, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. 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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 ******** 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 ****** 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? 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 ****** 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 ****** 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: All my comments have been addressed. Again I find the topic and the bayesian network approach really interesting very well presented. Reviewer #2: All comments addressed in the manuscript or adequately explained in the Author's response letter. The raw data has been made available (checked on Zenodo). ****** 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: Yes: Eleftherios Meletis Reviewer #2: No ******** https://doi.org/10.1371/journal.pone.0307041.r003
Formally Accepted
3 Jul 2024 Acceptance Letter - Liling Chaw, Editor PONE-D-24-17062R1 PLOS ONE Dear Dr. Huguet-Torres, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Liling Chaw Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0307041.r004

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