Low rate of SARS-CoV-2 incident infection identified by weekly screening PCR in a prospective year-long cohort study

Whitney E. Harrington; Winnie Yeung; Ingrid A. Beck; Fred D. Mast; John Houck; Sheila Styrchak; Leslie R. Miller; Song Li; Micaela Haglund; Yonghou Jiang; Blair Armistead; Jackson Wallner; Tina Nguyen; Daisy Ko; Samantha Hardy; Alyssa Oldroyd; Ana Gervassi; John D. Aitchison; Lisa M. Frenkel

doi:10.1371/journal.pone.0274078

Peer Review History

Original SubmissionJuly 8, 2022
29 Jul 2022 Decision Letter - A. M. Abd El-Aty, Editor PONE-D-22-19281Low rate of SARS-CoV-2 incident infection identified by weekly screening PCR in a prospective year-long cohort studyPLOS ONE Dear Dr. Frenkel, 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: As appended below, the reviewers have raised some concerns/critiques and suggested further justification/work to consolidate the findings. Do go through the comments and amend the MS accordingly. ============================== Please submit your revised manuscript by Sep 12 2022 11:59PM. 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Abd El-Aty 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. 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 the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ 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 Reviewer #3: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: N/A ****** 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: No ****** 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 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: The manuscript submitted by Frenkel et al and entitled “Low rate of SARS-CoV-2 incident infection identified by weekly screening PCR in a prospective year-long cohort study” evaluates the utility of asymptomatic screening for SARS-CoV-2 in low-risk populations. In this work 553 seronegative individuals were followed for 1 year and tested using self-collected nasal swabs for rtPCR testing. Of the subjects tested, only 9 cases were identified as positive and included subjects at greater risk, HCP, house member of a HCP, student, and daycare case. Furthermore, due to the once-a-week screening, 1 of 9 were identified prior to symptom onset and self-requested testing. Overall, the study is well written and demonstrates that in low risk, high educated settings, a weekly screening had low impact on identifying pre-symptomatic individuals. A few modifications should be addressed prior to publication. Major Comments What was the prevalence in the area during the period of testing and do you have that available for asymp vs symptomatic subjects (greater area vs study population). I would also suggest adding the date range to the materials and methods section. Minor Comments Ln 66: Why was transport media not used for the study and was there any stability testing done in house to demonstrate that dry swabs remained detectable over the 72 hours. Figure 1: What do the 2 no stars represent? Is that no specific variable determined? Conclusion: Add a limitation that contacts are all self-reported and as this was work done at a place of employment, individuals may have misrepresented their social interactions. Reviewer #2: This is a very interesting study providing intriguing evidence for the usefulness of the weekly testing with rtPCR. RTPCR has its limits due to the price and the need to purify the samples. In one recent study (PMID: 35395856), completely alternative approach was suggested with much faster turnaround time without compromising the quality, sensitivity and specificity. Maybe authors can elaborate the discussion about this point a bit more. Would the faster and cheaper testing method improve the proposed population surveillance outcomes? Reviewer #3: This is a very nice paper. Short Title: I think that shortening SARS-CoV-2 to SARS2 is unwise. Perhaps “rate of incident” can be changed to “incidence” to accommodate more complete nomenclature. Line 76: How was the sensitivity of detection for the nasal specimens determined? I think that it should be possible to address the HIPAA considerations in creating a deidentified public data set by replacing dates with the intervals between dates, and use of age groupings rather than age. This should represent sufficient deidentification. The questionairre data obviously constitutes identification, but the details are unimportant for purposes of this paper. ****** 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.0274078.r001
Revision 1
8 Aug 2022 Author Response Reviewers' Comments: Reviewer #1: The manuscript submitted by Frenkel et al and entitled “Low rate of SARS-CoV-2 incident infection identified by weekly screening PCR in a prospective year-long cohort study” evaluates the utility of asymptomatic screening for SARS-CoV-2 in low-risk populations. In this work 553 seronegative individuals were followed for 1 year and tested using self-collected nasal swabs for rtPCR testing. Of the subjects tested, only 9 cases were identified as positive and included subjects at greater risk, HCP, house member of a HCP, student, and daycare case. Furthermore, due to the once-a-week screening, 1 of 9 were identified prior to symptom onset and self-requested testing. Overall, the study is well written and demonstrates that in low risk, high educated settings, a weekly screening had low impact on identifying pre-symptomatic individuals. A few modifications should be addressed prior to publication. Major Comments What was the prevalence in the area during the period of testing and do you have that available for asymp vs symptomatic subjects (greater area vs study population). -We thank the reviewer for their feedback. The prevalence of symptomatic infection in the greater area (King County) varied across the year but reached a peak 7-day incidence of more than 200 cases / 100,000 population. This information is presented in the fourth paragraph of the discussion, along with a citation to the King County Department of Health website with full rolling incidence of infection throughout the pandemic. Unfortunately, to the best of our knowledge there were no large studies of asymptomatic individuals from the larger population during the time period of our study, so this information is not available for comparison. I would also suggest adding the date range to the materials and methods section. -We have moved the information on date range of enrollment from the first sentence of the Results to the first sentence of the Material and Methods. Minor Comments Ln 66: Why was transport media not used for the study and was there any stability testing done in house to demonstrate that dry swabs remained detectable over the 72 hours. -At the time of the study there were transport media shortages globally, so we conducted in house testing to demonstrate that dry swabs retained similar sensitivity up to 72 hours. Specifically, we compared the cycle threshold (Ct) values of nasal swabs spiked with 50ul of a SARS-CoV-2 positive specimen collected in universal transport medium (UTM), when held in UTM, PBS, or dry, and found that the cycle time remained stable over 72 hours regardless of storage condition. A comment noting this is now included in the Materials & Methods. Figure 1: What do the 2 no stars represent? Is that no specific variable determined? -We have clarified in the figure legend that “no stars” represents the two cases with no risk factor for infection identified. Conclusion: Add a limitation that contacts are all self-reported and as this was work done at a place of employment, individuals may have misrepresented their social interactions. -We have added these limitations to the conclusions. Reviewer #2: This is a very interesting study providing intriguing evidence for the usefulness of the weekly testing with rtPCR. RTPCR has its limits due to the price and the need to purify the samples. In one recent study (PMID: 35395856), completely alternative approach was suggested with much faster turnaround time without compromising the quality, sensitivity and specificity. Maybe authors can elaborate the discussion about this point a bit more. Would the faster and cheaper testing method improve the proposed population surveillance outcomes? -We appreciate the reviewer calling this publication to our attention. We have added a brief discussion of how alternative testing approaches may change the value of surveillance to the manuscript, citing this publication. Reviewer #3: This is a very nice paper. Short Title: I think that shortening SARS-CoV-2 to SARS2 is unwise. Perhaps “rate of incident” can be changed to “incidence” to accommodate more complete nomenclature. -We appreciate this feedback and have edited the Short Title to: “Low incidence of SARS-CoV-2 by weekly PCR” Line 76: How was the sensitivity of detection for the nasal specimens determined? -The sensitivity of detection was determined using 2-fold serial dilutions of an in-vitro transcribed SARS-CoV-2 RNA control spiked into SARS-CoV-2 negative nasal swab matrix (nasal swabs collected from healthy donors). The analytical sensitivity of the diagnostic RT-qPCR was estimated at 10 SARS-CoV-2 RNA copies/reaction (equivalent to 250 copies of SARS-CoV-2 per nasal swab eluted in 1 mL of PBS) utilizing a cycle threshold cut-off of 40. To confirm the limit of detection (LoD) we tested 20 replicate samples at 1x and 20 replicates at 2x the estimated LoD, resulting in 95% positive replicates at 250 copies/swab and 100% positivity at 500 copies/swab. We have included a brief description of our approach in the third paragraph of the Materials & Methods. I think that it should be possible to address the HIPAA considerations in creating a deidentified public data set by replacing dates with the intervals between dates, and use of age groupings rather than age. This should represent sufficient deidentification. The questionnaire data obviously constitutes identification, but the details are unimportant for purposes of this paper. -We appreciate this suggestion and have generated a primary data set with age blocks as suggested and vaccine dates removed, but compiled number of vaccinated individuals per week of the study presented. Attachments Attachment Submitted filename: SARS2_Prospective_Epi_ReviewerResponse_8Aug22.doc https://doi.org/10.1371/journal.pone.0274078.r002
23 Aug 2022 Decision Letter - A. M. Abd El-Aty, Editor Low rate of SARS-CoV-2 incident infection identified by weekly screening PCR in a prospective year-long cohort study PONE-D-22-19281R1 Dear Dr. Frenkel, 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, A. M. Abd El-Aty 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 #2: All comments have been addressed Reviewer #3: 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 #2: Yes Reviewer #3: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes Reviewer #3: (No Response) ****** 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 #2: Yes Reviewer #3: (No Response) ****** 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 #2: Yes Reviewer #3: (No Response) ****** 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 #2: (No Response) Reviewer #3: (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 #2: No Reviewer #3: No ******** https://doi.org/10.1371/journal.pone.0274078.r003
Formally Accepted
15 Sep 2022 Acceptance Letter - A. M. Abd El-Aty, Editor PONE-D-22-19281R1 Low rate of SARS-CoV-2 incident infection identified by weekly screening PCR in a prospective year-long cohort study Dear Dr. Frenkel: 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. A. M. Abd El-Aty Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0274078.r004

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