SARS-CoV-2 variant introduction following spring break travel and transmission mitigation strategies

Justin M. Napolitano; Sujata Srikanth; Rooksana E. Noorai; Stevin Wilson; Kaitlyn E. Williams; Ramses A. Rosales-Garcia; Brian Krueger; Chloe Emerson; Scott Parker; John Pruitt; Rachel Dango; Lax Iyer; Adib Shafi; Iromi Jayawardena; Christopher L. Parkinson; Christopher McMahan; Lior Rennert; Congyue Annie Peng; Delphine Dean

doi:10.1371/journal.pone.0301225

Peer Review History

Original SubmissionNovember 1, 2023
20 Dec 2023 Decision Letter - Vittorio Sambri, Editor PONE-D-23-32931SARS-CoV-2 variant introduction following spring break travel and transmission mitigation strategiesPLOS ONE Dear Dr. Peng, 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. Your manuscript has been revised by two experts in t he field and both of thema raised concerns abiut this paper. In particualr one of the reviewer suggested to reject the manuscript due to major weakness points (see the report form the reviewers for details about the concerns found). 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In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well. [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: No ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: No ****** 3. 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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: The manuscript is interesting but still needs some work to improve its impact. Napolitano and collaborators show the role that repetitive testing can play in transmission mitigation, reducing community spread of COVID-19 and identified that distantly related lineages were brought to the area after spring break travel of students. In the ethic statement the Authors declare: This study is retrospective and uses bioreposited de-identified samples and data. Patient identifier information were removed before SARS-CoV-2 sequencing and data analysis. Informed consent was waived by the Clemson University IRB committee. While at line 106-107 Authors state: we employed a comprehensive approach using saliva-based mass testing pre- and post-spring break. Again at line 146-147 Upon return to campus, all students were required to undergo testing So, it is not clear to me if the study was in fact retrospective or not, is samples collection part of this study or did the authors use bioreposited samples as declared in the ethics statement? If this is the case, I would suggest to shift the text lines 142-165 in the introduction as sample collection was not part of the study. The authors give some students’ demographic data such as age, gender and race, but it is not clear if these data have been very much analyzed e.g to compare groups is there any difference among groups in term of behavior, travel destinations etc Besides some more details and discussion on the vaccination status of the students would be welcome (was this information available?) Details and discussion about travelling destinations during the breaks would be needed. Did the students travel only nationally or also internationally? Did the Authors manage to collect information on COVID-19 VOCs from the areas visited by the students during the breaks? Is it possible to trace them back? Impact of the paper: The Authors conclude: We show the role that repetitive testing can play in transmission mitigation, reducing community spread, and maintaining in-person education. It is not clear how testing can play in transmission mitigation and reducing community spread are the authors suggesting to keep on testing students before and after breaks? What kind of measure can be implemented in case they will test positive if there are no longer isolation policies in place? “We identified that distantly related lineages were brought to the area after spring break travel regardless of the presence of a dominant variant of concern”. Since it is quite well established that travelling is one of the most important factor increasing virus diversity, are the authors able to identify any suggestions/solutions (eg for surveillance purposes, for disease management and control etc) based on their data, to reduce the spread of SARS_CoV-2 and other respiratory viruses to be implemented at the level of mobile communities such as university students, and the academic community as a whole? Reviewer #2: This work evaluates how students travelling during spring break may affect the university and surrounding communities, in terms of circulating variants and number of infections upon their return. The authors also discuss the role of repetitive testing as a mitigation strategy. Considering the sample size and timeframe of the study, I cannot recommend the publication of this work. The role travelling plays in importing new variants into communities has been vastly described already, including students on spring break, as referenced by the authors themselves. The same can be said on the importance of repetitive testing, which has been evaluated in the past in a range of settings, from schools, to local labour force, to nursing homes. Additionally, it is not clear whether the authors are suggesting coupling WGS with repetitive testing. While this certainly yields very useful information, it also slows down the turn around time considerably; this is crucial when advising health authorities on policies for mitigation and containment, especially when dealing with asymptomatic, highly mobile individuals. Unfortunately this study does not add enough significant info to the body of work on the subject, at present. ****** 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: Yes: Alessandra Scagliarini 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. 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.0301225.r001
Revision 1
8 Mar 2024 Author Response Dear Editor Thank you for the feedback on our manuscript titled “SARS-CoV-2 variant introduction following spring break travel and transmission mitigation strategies”. We are grateful for the valuable comments provided by the reviewers, and each of the comments is addressed in this letter. To summarize, we updated the manuscript to meet PLOS ONE’s style requirement, we added the statement to confirm that the revision does not alter our adherence to all PLOS ONE policies on sharing data and materials, we added the full ethics statement in the ‘Methods’ section, we added additional methodology, data, and figures suggested by the reviewers. Here are our point by point responses: 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. We updated our manuscript to comply with PLOS ONE’s style requirements. 2. Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” Here is the authors’ statement: “I have read the journal's policy and the authors of this manuscript have the following competing interests: SW is currently employed by Illumina. BK, SP, JP, RD, LI, and AS are employed by Labcorp. The other authors declare no competing interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials.” 3. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well. We added the following in the methods section: The study protocol was reviewed and approved by Clemson University Institutional Review Boards (IRB) (IRB# 2021-043-02). This study is retrospective and uses bioreposited de-identified samples and data. Patient identifier information were removed before SARS-CoV-2 sequencing and data analysis. Informed consent was waived by the Clemson University IRB committee. Review Comments to the Author Reviewer #1: The manuscript is interesting but still needs some work to improve its impact. Napolitano and collaborators show the role that repetitive testing can play in transmission mitigation, reducing community spread of COVID-19 and identified that distantly related lineages were brought to the area after spring break travel of students. In the ethic statement the Authors declare: This study is retrospective and uses bioreposited de-identified samples and data. Patient identifier information were removed before SARS-CoV-2 sequencing and data analysis. Informed consent was waived by the Clemson University IRB committee. While at line 106-107 Authors state: we employed a comprehensive approach using saliva-based mass testing pre- and post-spring break. Again at line 146-147 Upon return to campus, all students were required to undergo testing. So, it is not clear to me if the study was in fact retrospective or not, is samples collection part of this study or did the authors use bioreposited samples as declared in the ethics statement? If this is the case, I would suggest to shift the text lines 142-165 in the introduction as sample collection was not part of the study. Thanks for this comment. We moved the corresponding description of saliva sample collection and saliva testing to the introduction section. We also moved some information regarding 2022 sample collection to the same spot in the introduction as well. The authors give some students’ demographic data such as age, gender and race, but it is not clear if these data have been very much analyzed e.g to compare groups is there any difference among groups in term of behavior, travel destinations etc. Besides some more details and discussion on the vaccination status of the students would be welcome (was this information available?) This is a great comment. The data provided in this manuscript is a summary of the demographic information of the samples used for sequencing. We do not have any personal information on behavior and travel destinations as the samples were deidentified prior to sequencing and analysis. However, we did add analysis of social media data from the time period to get some average data on locations students went to for spring break. In addition, we analyzed tests from local community testing during the same time period as a comparison group. Local K-12 schools had different (later) spring break periods so that population was less likely to travel. Please See Table 2 and Supporting Fig 1. We published a separate paper (cited below) detailing the discussions on vaccines and the omicron variant. We made additional comments in the discussion. Rennert L, Ma Z, McMahan CS, Dean D. Covid-19 vaccine effectiveness against general SARS-CoV-2 infection from the omicron variant: A retrospective cohort study. PLOS Glob Public Health. 2023;3(1):e0001111. doi: 10.1371/journal.pgph.0001111. Epub 2023 Jan 10. PMID: 36777314; PMCID: PMC9910751. Details and discussion about travelling destinations during the breaks would be needed. Did the students travel only nationally or also internationally? This comment is very helpful. While we are unable to collect such information for individual patients as the individual samples were deidentified prior to analysis, we did do an additional analysis of social media for the period in question to get some information on student travel patterns for these spring breaks. Overall, from the social media analysis, the college student population mentions southeast beach destinations for travel (Florida and Miami were high resulting terms). There were no international destinations mentioned in the social media and international travel was also restricted especially during the 2021 spring break period so it is unlikely that this would contribute significantly the observed data. We added the information regarding the social media data, centering around a table (Table 2) we produced which ranked the prevalence of the words. We added the methodology for collecting this information in the method section. We added the word cloud figure in the supporting material (S1_Fig). Did the Authors manage to collect information on COVID-19 VOCs from the areas visited by the students during the breaks? Is it possible to trace them back? As mentioned above, while we are unable to collect the specific travel information of individual students, the social media analysis indicated that Florida (and Miami in particular) were likely to be popular destination. This is consistent with the VOC data recorded in the student population after spring break. Particularly in 2021, when new variants that had been circulating in Florida were found to be introduced in the student population after the spring break period. In addition, we have added the community sample sequenced data during that time frame for comparison. While the new VOCs did begin to circulate in that population the overall COVID rates remained consistent pre- and post-university spring break. Impact of the paper: The Authors conclude: We show the role that repetitive testing can play in transmission mitigation, reducing community spread, and maintaining in-person education. It is not clear how testing can play in transmission mitigation and reducing community spread are the authors suggesting to keep on testing students before and after breaks? What kind of measure can be implemented in case they will test positive if there are no longer isolation policies in place? “We identified that distantly related lineages were brought to the area after spring break travel regardless of the presence of a dominant variant of concern”. Since it is quite well established that travelling is one of the most important factor increasing virus diversity, are the authors able to identify any suggestions/solutions (eg for surveillance purposes, for disease management and control etc) based on their data, to reduce the spread of SARS_CoV-2 and other respiratory viruses to be implemented at the level of mobile communities such as university students, and the academic community as a whole? Thank you for pointing this out. We agree with the reviewer that it is important that our data could be used to suggest mitigation management. We are addressing this by supporting both the restrictions and level of seriousness that we took in 2021 vs 2022. Essentially, people took COVID more seriously in 2021. This was also supported by the social media analysis which noted that in 2021 terms about spring break were associated with terms about COVID restrictions and mitigation measures. In contrast terms about spring break in 2022 showed very little association with COVID mitigation measures. Of note, while COVID rates increased after the spring break period in the Clemson student population, this did not seem to translate to an increase in COVID rates in the community. This may indicate that while students do certainly bring back more infectious diseases from travel during spring break, they are not likely to be a significant source of spread to the immediate non-academic population. It was not clear if this was due to the associated mitigation measures (isolation and quarantine) implemented during the pandemic or due to lower rates of mingling between the local community and university populations. Reviewer #2: This work evaluates how students travelling during spring break may affect the university and surrounding communities, in terms of circulating variants and number of infections upon their return. The authors also discuss the role of repetitive testing as a mitigation strategy. Considering the sample size and timeframe of the study, I cannot recommend the publication of this work. The role travelling plays in importing new variants into communities has been vastly described already, including students on spring break, as referenced by the authors themselves. The same can be said on the importance of repetitive testing, which has been evaluated in the past in a range of settings, from schools, to local labour force, to nursing homes. Additionally, it is not clear whether the authors are suggesting coupling WGS with repetitive testing. While this certainly yields very useful information, it also slows down the turn around time considerably; this is crucial when advising health authorities on policies for mitigation and containment, especially when dealing with asymptomatic, highly mobile individuals. Unfortunately this study does not add enough significant info to the body of work on the subject, at present. We understand the concerns the reviewer has about our study. We addressed the concerns in this revision to our best given the limitations with the data we could acquire. Due to the limitations of available sequencing resources, the sequenced samples are randomly selected from the testing samples collected from college students (N=27 and N=101 for pre- and post-spring break in 2021, respectively; N=9 and N=18 for pre- and post-spring break in 2022). We added a cohort for university employees and unaffiliated community members 47 (9 university, 38 community) from pre-spring break 2021 and 101 (41 university, 60 community) from post-spring break 2021 for comparison purposes. The number of sequenced samples from university employees and community members was small due to few patients testing positive with COVID during the associated time period. The data was included in the supplemental materials. In addition, while we are not able to know exact travel plans of individual student patients as the samples were deidentified, we added data on social media analysis to gain a qualitative understanding of where the students were likely to travel during the associated time period. Although travel-related virus spreading has been documented and the importance of repetitive testing has been established, here, we are presenting a case study, that tracks a university population comprised of young individuals at low risk of hospitalization along the progression of the virus mutation during the pandemic and during the pandemic to endemic transition. We provide a model of the virus transmission in such a population using a highly calibrated phylogenetic tree assembly of a large amount of known virus lineage set ( > 2000 known virus lineage) in the midst of high virus gene pool diversity (year 2021) and low gene pool diversity (year 2022). The model has significance in both virus genetics and public health. We agree with the reviewer that it is crucial when advising health authorities on policies for mitigation and containment, especially when dealing with asymptomatic, highly mobile individuals. The case we presented here provides an example of surveillance of the population with testing in a large amount to slow down spreading, while using a randomly selected sample set for sequencing under resources and time limitations. We added social media data collection to strengthen our argument on the importance of testing and individual behaviors in virus mitigation. https://doi.org/10.1371/journal.pone.0301225.r002
13 Mar 2024 Decision Letter - Vittorio Sambri, Editor SARS-CoV-2 variant introduction following spring break travel and transmission mitigation strategies PONE-D-23-32931R1 Dear Dr. Peng, 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. Please make sure your user information is up-to-date by logging into Editorial Manager at http://www.editorialmanager.com/pone/ and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Vittorio Sambri, M.D., Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0301225.r003
Formally Accepted
26 Apr 2024 Acceptance Letter - Vittorio Sambri, Editor PONE-D-23-32931R1 PLOS ONE Dear Dr. Peng, 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 Professor Vittorio Sambri Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0301225.r004

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