Monitoring and responding to emerging infectious diseases in a university setting: A case study using COVID-19

K. James Soda; Xi Chen; Richard Feinn; David R. Hill

doi:10.1371/journal.pone.0280979

Peer Review History

Original SubmissionJanuary 19, 2023
12 Mar 2023 Decision Letter - Barbara T Rumain, Editor PONE-D-23-00956 Monitoring and responding to emerging infectious diseases in a university setting: A case study using COVID-19 PLOS ONE Dear Dr. Soda, 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 Apr 26 2023 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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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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? 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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors present a modified agent-based covid-19 model based on Covasim. The modifications are explained in detail and are based on disease mitigation strategies implemented by Quinnipiac University in the Fall 2020 semester. The results of the model are then compared to observed data from that semester. Suggestions for future infectious diseases at institutes of higher educations are also provided. The model and methodology for analyzing it appear sound and thorough. My main questions are regarding the main four scenarios: Can the authors provide the rationale for choosing the two specific R_0 values used in the study? Did these come from known values at the time or were they completely hypothetical? Also, the authors cite Bharti et al. for the average contact rates of 8 and 10, which was published in 2021. However, the authors state that their model was created in summer 2020 to help plan for fall 2020. Was the preprint mentioned in the Acknowledgments available to the authors for their initial use of the model? This point could be made clear. Reviewer #2: This manuscript provides insight into one university's experience with COVID-19 modeling and disease mitigation. It provides detailed information related to disease modeling strategies and observed disease transmission that would be useful to other IHEs for future use of Disease X modeling. Additionally, they present practical considerations related to university prevention strategies. Comparisons with other IHE experiences highlight similar strategies/outcomes as well as differing experiences that call for further investigation. To provide additional clarity for the reader in understanding the figures, the following edits are recommended: Given that Figure 1 includes predicted and observed values, include "predicted" in the manuscript description and the figure labeling. With regard to Figure 3, the manuscript text does state that the figure shows predicted values; adding this to the figure label would provide further clarity. Label y-axis for figures 1 and 3. 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 ******** 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.0280979.r001
Revision 1
12 Apr 2023 Author Response Responses to Reviewer #1 Comment: The authors present a modified agent-based covid-19 model based on Covasim. The modifications are explained in detail and are based on disease mitigation strategies implemented by Quinnipiac University in the Fall 2020 semester. The results of the model are then compared to observed data from that semester. Suggestions for future infectious diseases at institutes of higher educations are also provided. Response: We believe that this is an accurate summary of our work and goals. --------------------------------------------------------------------------------------------------------------- Comment: The model and methodology for analyzing it appear sound and thorough. Response: We thank the reviewer for this favorable assessment. --------------------------------------------------------------------------------------------------------------- Comment: My main questions are regarding the main four scenarios: Can the authors provide the rationale for choosing the two specific R_0 values used in the study? Did these come from known values at the time or were they completely hypothetical? Response: Our main four scenarios used two values for R0, 1.5 and 2.5. Both these values were informed and later validated by the literature. We selected the R0 value of 2.5 because the (US) Centers for Disease Control and Prevention’s COVID-19 Pandemic Planning Scenarios, as published on May 20, 2020, listed 2.5 as their best estimate for R0. In addition, Li et al. (2020) estimated a similar value for R0 (2.2) using case data in Wuhan, China from between December 10, 2019, and January 4, 2020. Our model did not directly use R0 as a model parameter. Instead, we used R0 to establish reasonable values for the probability that a social contact between an infectious individual and a susceptible individual would lead to disease transmission. However, we also believed that public health interventions, such as social distancing and masking, would also lower the probability of transmission. To account for these effects, we also incorporated scenarios where R0 was 1.5, partially in convention with one of the effective reproductive numbers used in Paltiel, Zheng, and Walensky (2020). Later, Pitzer et al.(2021) retroactively validated this choice through their estimates for the effective reproductive rate in the United States during the summer of 2020. The rationale provided above, along with the relevant citations, have now been added to the manuscript. (Relevant Page and Line in Manuscript with Tracked Changes: pg. 11, Lines 230-238) --------------------------------------------------------------------------------------------------------------- Comment: Also, the authors cite Bharti et al. for the average contact rates of 8 and 10, which was published in 2021. However, the authors state that their model was created in summer 2020 to help plan for fall 2020. Was the preprint mentioned in the Acknowledgments available to the authors for their initial use of the model? This point could be made clear. Response: The reviewer is correct that Dr. Bharti provided us with a preprint of her and her colleagues’ paper before it was published, and this preprint informed our work. We now explicitly state this in the main text. (Relevant Page and Line in Manuscript with Tracked Changes: pg. 11, Lines 238-240) ----------------------------------------------------------------------------------------------------------------- Response to Reviewer 2 Comment: This manuscript provides insight into one university's experience with COVID-19 modeling and disease mitigation. It provides detailed information related to disease modeling strategies and observed disease transmission that would be useful to other IHEs for future use of Disease X modeling. Additionally, they present practical considerations related to university prevention strategies. Comparisons with other IHE experiences highlight similar strategies/outcomes as well as differing experiences that call for further investigation. Response: We believe that this is an accurate summary of our work. --------------------------------------------------------------------------------------------------------------- Comment: To provide additional clarity for the reader in understanding the figures, the following edits are recommended: Given that Figure 1 includes predicted and observed values, include "predicted" in the manuscript description and the figure labeling. Response: We now explicitly mention that Figure 1 contains both predicted and observed values, both within the in-text description and in the figure title, and are more careful to differentiate predicted results from observed results. The figure legend has also been updated to emphasize that the median predictions and confidence intervals were based on the same 1,000 replicate simulations. (Relevant Page and Line in Manuscript with Tracked Changes: pg. 16, Lines 343-347; pg. 16, Lines 351-352; pg. 16, Line 354) --------------------------------------------------------------------------------------------------------------- Comment: With regard to Figure 3, the manuscript text does state that the figure shows predicted values; adding this to the figure label would provide further clarity. Response: Both the figure title and figure legend now explicitly state that Figure 3 shows predicted values. Just as in Figure 1, we also updated the legend to emphasize that the median predictions and confidence intervals were based on the same 1,000 replicate simulations. (Relevant Page and Line in Manuscript with Tracked Changes: pg. 19, Lines 407-408; pg. 19, Lines 410) --------------------------------------------------------------------------------------------------------------- Comment: Label y-axis for figures 1 and 3. Response: Figures 1 and 3 now have labelled y-axes. (Relevant Files: Fig1.tif; Fig3.tif) --------------------------------------------------------------------------------------------------------------- Additional Modifications Made While Proofreading and Double-Checking Citations In addition to the changes mentioned above, we have made the following additional modifications: --------------------------------------------------------------------------------------------------------------- 1. The phrase, “Relative to targeted sampling, complete sampling had 32.05 fewer infections at the under boundary under 8 contacts/day…”, has been corrected to say, “Relative to targeted sampling, complete sampling had 32.05 fewer infections at the upper boundary under 8 contacts/day…” (pg. 19, line 403). --------------------------------------------------------------------------------------------------------------- 2. We previously stated that Cas et al. (2021) discussed Furman University’s COVID-19 response. Although this is implied within the paper, the authors only state that they are describing the response of a college in South Carolina. We have therefore removed Furman University’s name to follow this convention (pg. 27, line 616; pg. 32, line 724). --------------------------------------------------------------------------------------------------------------- 3. We have updated our description of Muller and Muller’s (2021) results on pg. 31, Lines 696-697 to more accurately reflect the authors’ findings on the effectiveness of contact tracing relative to surveillance testing with complete or nearly complete sampling. The description previously read, “This intervention has a long and proven track record in public health policy, translates well to novel diseases, and was found to have a comparable effectiveness to surveillance testing with complete sampling in other modeling studies of COVID-19 (41).” The description now reads, “This intervention has a long and proven track record in public health policy, translates well to novel diseases, and was found to have a comparable effectiveness to surveillance testing with complete or nearly complete sampling in other modeling studies of COVID-19, at least under certain measures (44).” --------------------------------------------------------------------------------------------------------------- 4. In our S1 Appendix, we previously stated that a CDC seroprevalence study in Connecticut estimated that between 12.82% and 23.26% of all infections led to a reported case. A second review of the paper (Havers et al. 2020) found that it was actually between 12.61% and 22.77% of all infections. This statement has now been corrected (S1 Appendix, pg. 2, line 39). --------------------------------------------------------------------------------------------------------------- Attachments Attachment Submitted filename: SodaChenFeinnHill_PLOSOne_ResponseLetter.pdf https://doi.org/10.1371/journal.pone.0280979.r002
28 Apr 2023 Decision Letter - Barbara T Rumain, Editor Monitoring and responding to emerging infectious diseases in a university setting: A case study using COVID-19 PONE-D-23-00956R1 Dear Dr. Soda, 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, Barbara T Rumain, PhD Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0280979.r003
Formally Accepted
9 May 2023 Acceptance Letter - Barbara T Rumain, Editor PONE-D-23-00956R1 Monitoring and responding to emerging infectious diseases in a university setting: A case study using COVID-19 Dear Dr. Soda: 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 Dr. Barbara T Rumain Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0280979.r004

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