Incidence of SARS-CoV-2 infection among healthcare workers before and after COVID-19 vaccination in a tertiary paediatric hospital in Warsaw: A retrospective cohort study

Beata Kasztelewicz; Katarzyna Skrok; Julia Burzyńska; Marek Migdał; Katarzyna Dzierżanowska-Fangrat

doi:10.1371/journal.pone.0301612

Peer Review History

Original SubmissionDecember 2, 2023
23 Jan 2024 Decision Letter - Olatunji Matthew Kolawole, Editor PONE-D-23-40084Incidence of SARS-CoV-2 infection among healthcare workers before and after COVID-19 vaccination in a tertiary paediatric hospital in Warsaw: a retrospective cohort studyPLOS ONE Dear Dr. Kasztelewicz, 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. ACADEMIC EDITOR: Please attend to all comments made by Reviewers and make necessary review and/or reconstructions where needed. Please submit your revised manuscript by Mar 08 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. 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Olatunji Matthew Kolawole, Ph.D. Academic Editor PLOS ONE 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. 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: The article require some review and re-construction as indicated by 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: Partly Reviewer #2: Partly Reviewer #3: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes Reviewer #3: 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 Reviewer #3: 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: No Reviewer #2: Yes Reviewer #3: 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: Kasztelewicz et al. presented the data for healthcare workers during COVID-19. Authors need to present data tables and figures in the correct order. The results and discussion are very vast and need to be very precise and conclusive. Reviewer #2: This study investigates the Incidence of SARS-CoV-2 infection among HCWs before and after COVID-19 vaccination in Warsaw. My comments are as below: - First of all, the introduction has to be re-organized and clearly illustrated to readers regarding of incidence of SARS-CoV-2 infection not only among healthcare workers but also among normal populations before and after COVID-19 vaccination. - What is the novelty of this work? First time in the world? (I don’t think so!). In the region? - The tables of this work are informative, however the quality of 2provided figures are very low, therefore the authors should provide high quality figures. - I would suggest adding a general conclusion Figure according to your own result (like a graphical abstract) - The possibility of confounding in the results should be discussed. Reviewer #3: The manuscript presents a scientifically accurate evaluation of a retrospective analysis of the incidence of Covid-19 infections in health care workers before and after the provision of the SARS Cov-2 vaccine. Due to the analysis of retrospective data and the associated limitations in the availability and quality of the data and thus variables, no surprisingly new findings are presented. However, the manuscript is convincing due to the meticulous scientific processing, the comprehensive explanation of the statistical methods used, the transparency of the data through the extensive supplement and also through the critical, balanced discussion of the weaknesses of the author's own data and evaluation. Even after a literature search, I came to the conclusion that "this is the only study of the SARS-CoV-2 infection among HCWs in Poland and one of the few studies based on robust data obtained mainly from proactive universal screening PCR testing" There was only one passage where I would change the wording, line 55 "small cohorts". These cohorts had between >1000 and <1500 subjects. In line 59 +60, the reader learns that "we retrospectively analyzed the large real-world testing database"60 large real-world testing database". 60 large real-world testing database" with 2332 HCWs. Please reflect the ratio. The writing style is clear and the manuscript is well structured. This makes it very easy for the reader to follow. Perhaps the tables could be presented more compactly in the printed version. In principle, nothing stands in the way of publication. ****** 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 ******** [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. https://doi.org/10.1371/journal.pone.0301612.r001
Revision 1
5 Mar 2024 Author Response February 29, 2024 Olatunji Matthew Kolawole, PhD Academic Editor PLOS ONE Revision and resubmission of manuscript PONE-D-23-40084 Dear Dr. Olatunji Matthew Kolawole, Thank you for the opportunity to revise our manuscript on “Incidence of SARS-CoV-2 infection among healthcare workers before and after COVID-19 vaccination in a tertiary paediatric hospital in Warsaw: a retrospective cohort study”. We appreciate you and the reviewers for their time in reviewing our manuscript and providing valuable comments. The manuscript has been reviewed and adjusted to meet PLOS ONE’s style requirements, including those for file naming. The reference list has been thoroughly examined and updated (none of the references has been retracted). The figure files were uploaded to the PACE digital diagnostic tool. The figures are provided in tiff format with a resolution of 300 ppi. We have carefully addressed all the comments. Our point-by-point responses to the reviewers’ comments are provided below, and the online submission form will be updated accordingly. All line numbers refer to the revised manuscript with tracked changes. We appreciate your consideration and look forward to your response. Sincerely, Beata Kasztelewicz Corresponding Author Responses to the Reviewers’ comments on the manuscript: “Incidence of SARS-CoV-2 infection among healthcare workers before and after COVID-19 vaccination in a tertiary paediatric hospital in Warsaw: a retrospective cohort study”. Reviewer #1: Kasztelewicz et al. presented the data for healthcare workers during COVID-19. Authors need to present data tables and figures in the correct order. Thank you for this suggestion. To address this concern and clarify the Result section we split Figure 3 (Study Flowchart) into two figures separate for Phase 1 (Fig 3) and Phase 2 (Fig 4) of the study. We decided to maintain the order of the tables as we believe it is appropriate. The results and discussion are very vast and need to be very precise and conclusive. Thank you for this suggestion. We have considered all the above comments. We went through the Results and Discussion sections. We have added two subsections with informative headings (“Characteristics of the Study Population” and “SARS-CoV-2 RNA PCR testing”) in the Results section (lines 221 and 256, respectively). We have shortened and simplified Tables 2 and 3 by removing 10 and 4 rows, respectively. In addition, the Discussion section was shortened by removing following passage on line 436: “There are also some issues associated with massive asymptomatic testing that must be underlined. First, it requires additional operational and testing costs and a large laboratory capacity to provide rapid turnaround for testing. Second, the results of the PCR-based screening are valid only for the day of the test, which can cause a false sense of confidence[18]. Furthermore, the resources required to identify a single asymptomatic case are substantial and may not be cost-effective during a low prevalence period[19]. Thus, testing strategies should be implemented after careful consideration of resources, infrastructure capacity, and logistical issues[20]. In addition, the testing strategy must be guided by the local epidemiology, vaccination coverage, and efficacy among HCWs and in the community”. We hope that this clearly and concisely sets the information. Reviewer #2: This study investigates the Incidence of SARS-CoV-2 infection among HCWs before and after COVID-19 vaccination in Warsaw. My comments are as below: - First of all, the introduction has to be re-organized and clearly illustrated to readers regarding of incidence of SARS-CoV-2 infection not only among healthcare workers but also among normal populations before and after COVID-19 vaccination. Thank you for your suggestion. We have addressed this by removing the following passages from the Introduction section: on line 39: “…including universal masking, enhanced hand hygiene and personal protective equipment (PPE) training, symptom screening, and self-isolation of HCWs if symptomatic or in the case of close contact with an infected person”. and on line 44: “Following the implementation of COVID-19 vaccines, HCWs were among the first prioritised for vaccination in many countries, including Poland. Data from the placebo-controlled randomized phase 3 clinical trial of the Pfizer-BioNTech BNT162b2 vaccine showed 95% efficiency in preventing symptomatic SARS-CoV-2 infection [6]. Benefits similar to those observed in clinical trials were also observed in real-world conditions [7].” We also provided information on the number of SARS-CoV-2 infections in the general population during the study period (before and after the introduction of COVID-19 vaccination), as suggested. In particular, the following passage on lines 45-54 has been added: “In Poland, COVID-19 vaccination programme started on December 27, 2020, using the Pfizer-BioNTech BNT162b2 vaccine. HCWs were among the initial groups that prioritized for vaccination. The introduction of vaccination in Poland coincided with the descending phase of the second wave of the pandemic. At the end of December 2020, 1,289,293 COVID-19 cases were reported in Poland. Masovian Voivodeship was the region most affected by COVID-19, with Warsaw having the highest number of infections, with 64,813 confirmed cases by the end of 2020 [6,7]. Between February and April 2021, Masovian Voivodeship, like the rest of Poland, experienced a third wave of pandemics, with a peak of 5,264 daily cases reached on March 26, 2021. The number of cases decreased by June 2021, and by the end of August 2021, there were 45 daily cases of SARS-CoV-2 infections in Masovian Voivodeship [7,8]. We believe that this in the Introduction section provides an additional context to the reader. Regarding infection prevalence among HCWs, there are no official reports available for Poland (which was one of the rationales for our study). In the Introduction section, we have added the following passage with the results of an early report by Papoutsi et al. (i.e., before April 17, 2020) on the prevalence of infections among HCWs in different regions of the world, including Poland - lines 55-71: ” An early report on the global burden of the COVID-19 pandemic on HCWs showed high variability in HCW infection percentage among total case across regions, with a median of 10.04% and range from 0 to 24.09%. Of note, Poland was one of the countries with high percentage of HCWs infections accounting for 17.07% of cases [9].” Data on infections among HCWs in the European region later in the pandemic are limited, and we have highlighted this issue in the Introduction section. - What is the novelty of this work? First time in the world? (I don’t think so!). In the region? Thank you for pointing this out. We respond by adding the following passage to the Discussion on lines 584-585: “In summary, our data adds new knowledge regarding the incidence of SARS-CoV-2 infection among HCWs at the largest paediatric tertiary hospital in Poland, in the pre- and post-vaccination periods.” In addition, a passage on lines 576-578 was rephrased to underline that “this is the only study of SARS-CoV-2 infection among HCWs conducted in the central-east region of Poland and one of the few studies based on robust data obtained mainly from proactive universal screening by PCR testing”. - The tables of this work are informative, however the quality of 2 provided figures are very low, therefore the authors should provide high quality figures. Thank you for pointing this out. We have provided high-quality figures as suggested. All figures were verified using the PACE digital diagnostic tool. The figures are provided in tiff format, with resolution of 300 ppi. - I would suggest adding a general conclusion Figure according to your own result (like a graphical abstract) Thank you for the suggestion. We have prepared a graphical abstract for our study, which will be submitted as a PDF file. - The possibility of confounding in the results should be discussed. Thank you for pointing this out. We addressed confounding in the Discussion section describing the limitations of the study. To highlight this, we rephrase the passage on lines 546-552 as follows “Third, potential confounders may be present that were unaccounted for in the regression analyses (such as comorbidities, contact time with COVID-19 cases, movement of HCWs between high- and low-risk wards, compliance with PPE, or household-related factors) due to data limitations, and therefore the results deserves caution interpretation and may not generalise to other settings with different characteristics.” Reviewer #3: The manuscript presents a scientifically accurate evaluation of a retrospective analysis of the incidence of Covid-19 infections in health care workers before and after the provision of the SARS Cov-2 vaccine. Due to the analysis of retrospective data and the associated limitations in the availability and quality of the data and thus variables, no surprisingly new findings are presented. However, the manuscript is convincing due to the meticulous scientific processing, the comprehensive explanation of the statistical methods used, the transparency of the data through the extensive supplement and also through the critical, balanced discussion of the weaknesses of the author's own data and evaluation. Even after a literature search, I came to the conclusion that "this is the only study of the SARS-CoV-2 infection among HCWs in Poland and one of the few studies based on robust data obtained mainly from proactive universal screening PCR testing" We would like to thank the reviewer for the considerable time, effort, and suggestions for improving the quality of this paper. There was only one passage where I would change the wording, line 55 "small cohorts". These cohorts had between >1000 and <1500 subjects. In line 59 +60, the reader learns that "we retrospectively analyzed the large real-world testing database"60 large real-world testing database". 60 large real-world testing database" with 2332 HCWs. Please reflect the ratio. Thank you for pointing this out. We agree that the statements in the paragraph have been misleading. We have revised the paragraph and removed “in small cohorts of HCWs on line 75 and “large” on line 78. The writing style is clear and the manuscript is well structured. This makes it very easy for the reader to follow. Perhaps the tables could be presented more compactly in the printed version. In principle, nothing stands in the way of publication. Thank you again. The tables have been simplified, as suggested. In particular, Tables 2 and 3 were shortened by removing 10 and 4 rows, respectively. We believe this makes them more concise. Attachments Attachment Submitted filename: Response to reviewers.doc https://doi.org/10.1371/journal.pone.0301612.r002
20 Mar 2024 Decision Letter - Olatunji Matthew Kolawole, Editor Incidence of SARS-CoV-2 infection among healthcare workers before and after COVID-19 vaccination in a tertiary paediatric hospital in Warsaw: a retrospective cohort study PONE-D-23-40084R1 Dear Dr. Kasztelewicz, 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 Editorial Manager® , 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, Olatunji Matthew Kolawole, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0301612.r003
Formally Accepted
13 May 2024 Acceptance Letter - Olatunji Matthew Kolawole, Editor PONE-D-23-40084R1 PLOS ONE Dear Dr. Kasztelewicz, 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. Olatunji Matthew Kolawole Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0301612.r004

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 .