COVID-19 cases among medical laboratory services staff in South Africa, 2020–2021: A cohort study

Kerry Sidwell Wilson; Vusi Ntlebi; Felix Made; Natasha Sanabria; Melissa Vetten; Jitcy Joseph; Graham Chin; David Jones; Nonhlanhla Tlotleng

doi:10.1371/journal.pone.0268998

Peer Review History

Original SubmissionSeptember 13, 2021
31 Jan 2022 Decision Letter - Massimiliano Galdiero, Editor PONE-D-21-29566COVID-19 cases among medical laboratory services staff in South Africa, 2020-2021: A Cohort Study.PLOS ONE Dear Dr. Kerry Sidwell Wilson, 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 Mar 17 2022 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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We will update your Data Availability statement to reflect the information you provide in your cover letter. 4. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please delete it from any other section. [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: No ****** 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: COVID-19 cases among medical laboratory services staff in South Africa, 2020-2021: A Cohort Study. Technical Comments to the Author The manuscript is written in clear and understandable English and the final message is very strong. Remarks to the Author I suggest minor comments. Minor comments 1. Remove point from the title. The title should be “COVID-19 cases among medical laboratory services staff in South Africa, 2020-2021: A Cohort Study” 2. Report in the materials and methods section a paragraph on the inclusion and exclusion criteria used in the study. 3. Move limitations to the Materials and Methods section. 4. A better description of the study population is needed. Include Supplementary Table 1 as Table 1 in the manuscript and comment on it in the results section. 5. Indicate occupations with risk scores below 0.5 excluded from the analysis. 6. The description of the results needs to be improved. For example, figure 2 shows the incidence rates of infection among medical laboratory service personnel by gender, not all data are commented on in the text. 7. The captions of the figures appear within the text. They should be placed at the end of the paragraph in which the figure is cited. 8. Improve the resolution of the figures. 9. Change HCWS to HCWs in conclusion part (line 460). 10. HCWs has been critical for monitoring COVID-19 infections and other diseases, not for diagnosis. Please correct (lines 460-461). Reviewer #2: Summary: The aim of this study was to show an increased risk of COVID-19 for Medical laboratory workers. Records of COVID-19 laboratory-confirmed positive, in twelve months, were present in System (OHASIS). The results showed that some categories of medical laboratory staff are at increased risk for COVID-19, with the most increased risk were laboratory managers, confirms this is a complex interaction between workplace risk factors. This article is very interesting for the public of this journal. The language of paper is difficult to understand and includes many errors, and the results must be better reported. The main text and the data analysis have to need to improve. 1) In Abstract, result section: “… A total of 2091 COVID-19 positive cases (26% of staff) were reported via OHASIS over the twelve months’ period. Already present in materials and methods. i.e.,967 (46% of total cases), write in full i.e., write in full ei, such as reported is little clary. ...The number of COVID-19 cases was higher in first wave, i.e.,967 (46% of total cases) than in the second wave 846 (40% of total cases)...this part is very confusional; improve, for example putting the fraction in the parenthesis, and number percentual out of them, n% (n°/n. tot). 2) Line 133: we are missing parentheses and not in Grasset character. 3) Improve the introduction reporting similar studies. 4) Line 293: delete r, before the point.. 5) Line 368: 1 min, no 1m. 6) Line 429, 460: correct it . 7) Improve the figures, and in my opinion it would be better to remove the totals bar. ****** 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
24 Feb 2022 Author Response Revision Letter Thank you for allowing us to revise the manuscript and resubmit. We confirm that we have addressed each of the Reviewer’s comments (please see details below). We have also ensured that the manuscript meets the PLOS ONE style requirements. In addition, we have updated the Methods section to include the Data Availability statement. The ethics statement has also been moved to the Methods section, as requested. We have provided the images, as requested. Journal Requirements 1. Style – The submission style was updated to match the formatting guidelines. 2. Competing interests: One author is involved in establishing the information system used here to provide the data in the local government health departments. This does not alter our adherence to PLOS ONE policies on sharing data and materials. Deidentified participant data containing possibly identifiable data and personal medical data may be obtained on application to the National Health Laboratory Services and with compliance to their requirements and the POPI Act South Africa 2021. The application may be made on registering at https://aarms.nhls.ac.za/NHLS_AARMS/Public/Default.aspx 3. Data availability - Deidentified participant data may be obtained from the National Health Laboratory Services on application and compliance with their requirements. https://aarms.nhls.ac.za/NHLS_AARMS/Public/Default.aspx 4. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please delete it from any other section. – ethics statement removed from Acknowledgements and stated in Methods section Reviewers Comments Reviewer #1: COVID-19 cases among medical laboratory services staff in South Africa, 2020-2021: A Cohort Study. Technical Comments to the Author The manuscript is written in clear and understandable English and the final message is very strong. Thank you for this view Remarks to the Author Minor comments 1. Remove point from the title. The title should be “COVID-19 cases among medical laboratory services staff in South Africa, 2020-2021: A Cohort Study” Point removed, title now reads “COVID-19 cases among medical laboratory services staff in South Africa, 2020-2021: A cohort study” 2. Report in the materials and methods section a paragraph on the inclusion and exclusion criteria used in the study. The paragraph below on population was included in the Methods section, i.e., “Population All NHLS staff, including contract workers and experiential students, may report incidents to the surveillance system and, thus, be included in this study. Managers, safety health and environment staff and occupational health nurses may also report incidents reported to them on the surveillance system. Thus, all staff were eligible to be included in this analysis. Inclusion criteria: • Reported case on OHASIS • Employed, working or visiting at one of the medical laboratory facilities Exclusion criteria Age less than 18 years” 3. Move limitations to the Materials and Methods section. Limitations paragraph moved from the Discussion section to the Methods section A better description of the study population is needed. Include Supplementary Table 1 as Table 1 in the manuscript and comment on it in the results section. Table S1 moved to results section and renamed Table 1. We then included in the results section “The medical laboratory service employs mainly females (68.1%), but no significant relationship was seen between sex and COVID-19 cases in the staff (AOR 0.93 95% CI 0.83 - 1.03). All race groups were represented, where African workers represented 75.5% of the staff. Compared to Caucasian workers, African and Coloured workers had significantly increased odds of COVID-19 infection. The majority of workers were between 30 and 49 years of age (60.8%) and all age groups compared to those less than 29 years showed significantly increased odds of infection. Odds of infection varied significantly between some provinces, with the Eastern Cape reporting the highest odds compared to Gauteng province. (Table 1)” All following table numbers were also updated. 4. Indicate occupations with risk scores below 0.5 excluded from the analysis. Although the “COVID-19 Risk Score” that was based on US data excluded jobs with a risk score below 0.5 from further analysis (Table 3), none of the occupations listed in South African OHASIS dataset were excluded from analysis, where occupations with few employees were grouped into similar occupation groups (Table 2). This statement has been added to the main text. 6. The description of the results needs to be improved. For example, figure 2 shows the incidence rates of infection among medical laboratory service personnel by gender, not all data are commented on in the text. No difference in the incidence rates between men and women was seen. This statement has been added to the main text. 7. The captions of the figures appear within the text. They should be placed at the end of the paragraph in which the figure is cited. The caption for Fig 1 moved to below the paragraph it is first mentioned in. The remaining two figure captions are correctly placed. 8. Improve the resolution of the figures. Thank you for noticing. The resolution has been improved to 300dpi 9. Change HCWS to HCWs in conclusion part (line 460). Thank you for catching this typo. It has been corrected to HCWs. 10. HCWs has been critical for monitoring COVID-19 infections and other diseases, not for diagnosis. Please correct (lines 460-461). Diagnosing removed from the sentence. Reviewer #2: Summary: The aim of this study was to show an increased risk of COVID-19 for Medical laboratory workers. Records of COVID-19 laboratory-confirmed positive, in twelve months, were present in System (OHASIS). The results showed that some categories of medical laboratory staff are at increased risk for COVID-19, with the most increased risk were laboratory managers, confirms this is a complex interaction between workplace risk factors. This article is very interesting for the public of this journal. The language of paper is difficult to understand and includes many errors, and the results must be better reported. The main text and the data analysis have to need to improve. Thank you for your comments. We have completed a spell check to correct spelling errors and have revised grammatical mistakes where needed. The results section has been revised. 1) In Abstract, result section: “… A total of 2091 COVID-19 positive cases (26% of staff) were reported via OHASIS over the twelve months’ period. Already present in materials and methods. Sentence changed to: A total of 2091 (26% of staff) COVID-19 positive cases were reported. i.e.,967 (46% of total cases), write in full i.e., write in full ei, such as reported is little clary. ...The number of COVID-19 cases was higher in first wave, i.e.,967 (46% of total cases) than in the second wave 846 (40% of total cases)...this part is very confusional; improve, for example putting the fraction in the parenthesis, and number percentual out of them, n% (n°/n. tot). Thank you for your suggestion. The sentence was corrected to “The number of COVID-19 cases was higher in the first wave at 46%(967/2091) of cases, than in the second wave 40% (846/2091) of cases”. 2) Line 133: we are missing parentheses and not in Grasset character. Parentheses included, I am unfortunately not familiar with Grasset characters. 3) Improve the introduction reporting similar studies. Thank you for this suggestion. Currently this is the only report of COVID-19 incidence in South Africa focusing on the subcategories of health workers, such as medical laboratory workers. 4) Line 293: delete r, before the point.. Thank you for your suggestion. The sentence was deleted 5) Line 368: 1 min, no 1m. The abbreviation was corrected to 1 metre 6) Line 429, 460: correct it . Line 429 corrected to “These are recommendations that could be implemented within the South African context.” Line 460 corrected to “HCWs, specifically medical laboratory services staff, have been crucial to monitoring COVID-19 infections and other diseases” 7) Improve the figures, and in my opinion it would be better to remove the totals bar. Thank you for your comment. The totals bar was removed from Fig 2 and the resolution improved to 300dpi in all figures. Attachments Attachment Submitted filename: Revision_Letter_PLOSone.docx https://doi.org/10.1371/journal.pone.0268998.r002
13 May 2022 Decision Letter - Massimiliano Galdiero, Editor COVID-19 cases among medical laboratory services staff in South Africa, 2020-2021: A Cohort Study PONE-D-21-29566R1 Dear Dr. Sidwell Wilson, 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, Massimiliano Galdiero, M.D., Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): 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 ******** 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: The authors have adequately addressed the comments raised in the review process and I believe this manuscript is improved and acceptable for publication. Reviewer #2: (No Response) ****** 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: No https://doi.org/10.1371/journal.pone.0268998.r003
Formally Accepted
10 Jun 2022 Acceptance Letter - Massimiliano Galdiero, Editor PONE-D-21-29566R1 COVID-19 cases among medical laboratory services staff in South Africa, 2020-2021: A cohort study Dear Dr. Wilson: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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 Prof. Massimiliano Galdiero Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0268998.r004

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