COVID-19 reinfection in Liberia: Implication for improving disease surveillance

Godwin E. Akpan; Luke Bawo; Maame Amo-Addae; Jallah Kennedy; C. Sanford Wesseh; Faith Whesseh; Peter Adewuyi; Lily Sanvee-Blebo; Joseph Babalola; Himiede W. W. Sesay; Trokon O. Yeabah; Dikena Jackson; Fulton Shannon; Chukwuma David Umeokonkwo; Abraham W. Nyenswah; Jane Macauley; Wilhelmina Jallah

doi:10.1371/journal.pone.0265768

Peer Review History

Original SubmissionNovember 12, 2021
11 Jan 2022 Decision Letter - Siew Ann Cheong, Editor PONE-D-21-36066COVID-19 reinfection in Liberia: implication for improving disease surveillancePLOS ONE Dear Dr. Akpan, 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. Specifically, Reviewer 1 questioned how generalizable the results from a single county can be, and requested for an analysis of the spatial clustering of cases. Please address these, and other comments from the reviewers. Please submit your revised manuscript by Feb 25 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. 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, Siew Ann Cheong, 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 amend your current ethics statement to address the following concerns: a) Did participants provide their written or verbal informed consent to participate in this study? b) If consent was verbal, please explain i) why written consent was not obtained, ii) how you documented participant consent, and iii) whether the ethics committees/IRB approved this consent procedure. 3. We note that Figures 2 and 4 in your submission contain map/satellite images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission: a) You may seek permission from the original copyright holder of Figures 2 and 4 to publish the content specifically under the CC BY 4.0 license. We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text: “I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.” Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission. In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].” b) If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only. The following resources for replacing copyrighted map figures may be helpful: USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/ The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/ Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/ Landsat: http://landsat.visibleearth.nasa.gov/ USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/# Natural Earth (public domain): http://www.naturalearthdata.com/ [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: No Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No 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: 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: As mentioned, more than 80% cases occurred in one county and 86% cases of reinfection from the same county. The generalizability of this data for the whole country is questionable. As data on geolocation was available, Moran’s Index should have been calculated - clustering for events? Majority of reinfection cases were international travelers - How was international travel defined? Details related to in country measures to mitigate spread of COVID-19 will aid in better understanding of the scenario. Reviewer #2: Seems like an interesting article. Few suggestions: 1. PAGE 8 - LINE 11 - we can remove the word "got sick' in bracket. 2. In discussion, kindly add few points on the necessity of having Advanced labs in developing countries to get the genome sequencing done so that we can easily assess who will respond to which Cocktail antibody therapy. ****** 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: Mohan Kumar Reviewer #2: Yes:** Dr Sayak Roy [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.0265768.r001
Revision 1
16 Feb 2022 Author Response Editor's comment: 1. Specifically, Reviewer 1 questioned how generalizable the results from a single county can be, and requested for an analysis of the spatial clustering of cases. Please address these, and other comments from the reviewers Response: Thank you for the thorough review of our manuscript and for useful suggestions to improve the understanding of the work. We have carefully gone through the comments and made modifications as suggested in the work. We have also responded to the comments here for ease of reference to the changes made in the work. We hope that the work is now acceptable for publication and will be available to respond to further clarification, if any. Journal 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. Response: Thank you for the support link. We have used the attached link to format the manuscript to meet PLOS ONE’s style requirements. 2. Please amend your current ethics statement to address the following concerns: a) Did participants provide their written or verbal informed consent to participate in this study? b) If consent was verbal, please explain i) why written consent was not obtained ii) how you documented participant consent, and iii) whether the ethics committees/IRB approved this consent procedure. Response: Thank you for pointing out this. Written informed consent was obtained from the cases. This has been updated in the ethical consideration section of the work. [Lines 160 and 161] 3. We note that Figures 2 and 4 in your submission contain map/satellite images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission Response: Figures 2 and 4 were maps created by the authors for the work using ArcGIS Pro Version 2.8.2. They are not copyrighted materials, and so they do not need copyright permission. They can be published under the creative commons attribution license (CC BY 4.0). Reviewer 1: 1. As mentioned, more than 80% cases occurred in one county and 86% cases of reinfection from the same county. The generalizability of this data for the whole country is questionable. Response: Thank you for these points. The authors did not set out to make generalizations but rather describe the patterns of reinfection observed in the routine surveillance data and make a case for providing laboratory capacity for genomic sequencing in the country. To address the concern raised, the authors have added a section to assess the spatial pattern of distribution of the cases [Lines 130-145]. It is also important to note that: 1. Montserrado County accounts for the majority of the population of Liberia's 5.2 million. Of the 3,476,608 population of Liberia based on the 2008 census, Montserrado County made up 1,118,241 (32.2%) of the 15 counties. https://www.lisgis.net/page_info.php?7d5f44532cbfc489b8db9e12e44eb820=MzQy 2. Considering the high rates (77%) of reinfection among [international travelers, the hub of travel is Montserrado with the only two international airports. Additionally, the dense population and high community transmission and traditional family and friends contacts in Montserrado means that those travelers also made contacts with others in Montserrado County 3. The authors have analyzed several data points and provided reports to key stakeholders that have shown that Montserrado County data can be generalizable to a greater extent to the rest of Liberia on several attributes, including testing, cases, contacts, hospitalization. 2. As data on geolocation was available, Moran’s Index should have been calculated - clustering for events? Response: An additional section to address this has been added, and it reads, “To assess the overall distribution pattern of COVID-19 cases across the country – whether clustered, dispersed, or random, we used Spatial Autocorrelation (Global Moran's I). We used Cluster and Outlier Analysis (Anselin Local Moran's I) to identify the specific area and how the pattern exists. With the null hypothesis that the pattern is random or that no spatial autocorrelation is present in the transmission or distribution of the COVID-19 cases, we applied Global Moran's I in three different Input Feature Classes: county, district, and the location of individual cases (point). In the same vein, we applied Local Moran's I in two different Input Feature Classes: district and point. To ascertain the influence of COVID-19 cases on nearby neighboring or distant cases (target feature), we selected an Inverse Distance Conceptualization of Spatial Relationships with Euclidean Distance method in the Global Moran's I tool. We also set the same parameters as in Global Moran's I for Local Moran's I, with Row standardization and 999 Permutations to improve the precision of the pseudo p-value and the random distribution of cases.” The results of the analysis have also been added to the work. [Lines 186-201] 3. Majority of reinfection cases were international travelers - How was international travel defined? Response: The authors defined international travelers as “citizens who visited and returned from other countries or non-citizens who came into the country either by land border crossing, sea or flight.” This has been added to the work. [Lines 80-82] Review 2: 1. PAGE 8 - LINE 11 - we can remove the word "got sick' in bracket Response: The correction has been effected as suggested. [Line 44] 2. In discussion, kindly add few points on the necessity of having Advanced labs in developing countries to get the genome sequencing done so that we can easily assess who will respond to which Cocktail antibody therapy. Response: Thank you for this suggestion. The authors have added a few more comments to buttress the need for genomic sequencing. [Lines 249-253] Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0265768.r002
8 Mar 2022 Decision Letter - Siew Ann Cheong, Editor COVID-19 reinfection in Liberia: implication for improving disease surveillance PONE-D-21-36066R1 Dear Dr. Akpan, 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, Siew Ann Cheong, 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: (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: Yes:** Mohan Kumar https://doi.org/10.1371/journal.pone.0265768.r003
Formally Accepted
15 Mar 2022 Acceptance Letter - Siew Ann Cheong, Editor PONE-D-21-36066R1 COVID-19 Reinfection in Liberia: Implication for Improving Disease Surveillance Dear Dr. Akpan: 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. Siew Ann Cheong Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0265768.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 .