Evaluation of the United States COVID-19 vaccine allocation strategy

Md Rafiul Islam; Tamer Oraby; Audrey McCombs; Mohammad Mihrab Chowdhury; Mohammad Al-Mamun; Michael G. Tyshenko; Claus Kadelka

doi:10.1371/journal.pone.0259700

Peer Review History

Original SubmissionAugust 16, 2021
13 Oct 2021 Decision Letter - Martial L Ndeffo Mbah, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-21-26548Evaluation of the United States COVID-19 Vaccine Allocation StrategyPLOS ONE Dear Dr. Kadelka, 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 Nov 27 2021 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. 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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. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 3. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 4. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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. Additional Editor Comments: Please, address the handful of minor comments and suggestions of Reviewer 2. [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: No Reviewer #2: 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 ****** 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: In the present paper, the authors present their study about evaluating the Vaccine allocation strategy implemented by the Centers for Disease Control (CDC) in the US. This subject is of great importance in present times since the vaccine administration has started worldwide. Therefore, it is crucial to have instruments to monitor the vaccination campaign. The study design and methodology are well structured and clearly explained. The results and conclusions are well presented and thoroughly discussed. Therefore, the present study may be of great help in optimising the vaccination strategy in different countries. The description of the compartmental model and the calibration procedure is very precise, and the discussion of the parameters is exhaustive. Overall, the paper is well written and well organised. My only concern is relative to the code availability; no Python code is available at the address https://github.com/ckadelka/COVID19-CDC-allocation-evaluation reported in the text. Therefore, the decision is to accept the paper in the present form only after the python source codes are available. Reviewer #2: Using mathematical modeling, this manuscript analyzes if the strategy of vaccine allocation followed in the United States was suitable in terms of certain objective functions such as minimizing the number of deaths and the number of cases. The authors find that such strategy was not precisely optimum but performed similarly to the optimum strategies (for each objective function). In general, the manuscript is very well written, complete, and relevant. I am convinced that the translation of this model to other scenarios (for example other epidemic episodes ad regions) can be extremely helpful to guide public health policy in vaccination matters. As any modelling exercise, the authors are forced to propose simplifications and state uncorroborated assumptions to arrive to solutions. This is perfectly understandable. To me, the assumptions of the model seem appropriate. In sum, I find this paper truly interesting and well executed. Congratulations. Some recommendations follow: (a) To me, the clinical and epidemiological information presented in table 1 (i.e., info relevant to set the values of the model parameters) should be presented within the main text. (b) Similarly, I recommend moving the scheme in S1 Figure to the main text. (c) Line 105: “If solely incidence is minimized irrespective of YLL and mortality, then this group 105 should be vaccinated before older individuals with comparably fewer contacts”. Please clarify/elaborate. (d) Line 118: “Interestingly however, if vaccination does not reduce virus spread (fV = 1) other than through a reduction of infections, prioritization of elderly people becomes 119 less important as the vaccine does not act as a barrier to infection among the elderly”…. This statement unclear to me. Please elaborate and discuss…. (e) Line 146: The following statement can be misleading: “The higher the relative contagiousness of vaccinated individuals, the higher was the influence of vaccine function on mortality; if vaccinated individuals did not cause any new infections, vaccine function had no noticeable effect on mortality”. This can be understood in a general sense: vaccination does not decrease mortality. Please reformulate to convey the sense of comparison…. ****** 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
14 Oct 2021 Author Response Please see the attached Word document, which distinguishes reviewer comments and our response and edits by color. Here, the plain txt version: Reviewer #1: In the present paper, the authors present their study about evaluating the Vaccine allocation strategy implemented by the Centers for Disease Control (CDC) in the US. This subject is of great importance in present times since the vaccine administration has started worldwide. Therefore, it is crucial to have instruments to monitor the vaccination campaign. The study design and methodology are well structured and clearly explained. The results and conclusions are well presented and thoroughly discussed. Therefore, the present study may be of great help in optimising the vaccination strategy in different countries. The description of the compartmental model and the calibration procedure is very precise, and the discussion of the parameters is exhaustive. Overall, the paper is well written and well organised. My only concern is relative to the code availability; no Python code is available at the address https://github.com/ckadelka/COVID19-CDC-allocation-evaluation reported in the text. Therefore, the decision is to accept the paper in the present form only after the python source codes are available. We thank the reviewer for their positive assessment of our work. At the same time, we apologize for the oversight on our end. We simply forgot to upload the Python code to the GitHub repository, https://github.com/ckadelka/COVID19-CDC-allocation-evaluation. It is now uploaded. Reviewer #2: Using mathematical modeling, this manuscript analyzes if the strategy of vaccine allocation followed in the United States was suitable in terms of certain objective functions such as minimizing the number of deaths and the number of cases. The authors find that such strategy was not precisely optimum but performed similarly to the optimum strategies (for each objective function). In general, the manuscript is very well written, complete, and relevant. I am convinced that the translation of this model to other scenarios (for example other epidemic episodes ad regions) can be extremely helpful to guide public health policy in vaccination matters. As any modelling exercise, the authors are forced to propose simplifications and state uncorroborated assumptions to arrive to solutions. This is perfectly understandable. To me, the assumptions of the model seem appropriate. In sum, I find this paper truly interesting and well executed. Congratulations. We also thank this reviewer for their positive assessment of our study. Below, we describe how we addressed the particular recommendations. Some recommendations follow: (a) To me, the clinical and epidemiological information presented in table 1 (i.e., info relevant to set the values of the model parameters) should be presented within the main text. We followed the reviewer’s recommendation and moved the table with the model parameters into the main text (what used to be S1 Table is now Table 1). (b) Similarly, I recommend moving the scheme in S1 Figure to the main text. Again, we followed the reviewer’s recommendation and moved S1 Figure to the main text (what used to be S1 Figure is now Figure 1). (c) Line 105: “If solely incidence is minimized irrespective of YLL and mortality, then this group 105 should be vaccinated before older individuals with comparably fewer contacts”. Please clarify/elaborate. We clarified the sentence by (i) explicitly stating that minimizing incidence is the same as minimizing cases, and (ii) explicitly referencing the specific sub-populations in Table 1 (now Table 2) that are compared here: sub-population 8, which falls into phase 3 when minimizing cases/incidence and sub-populations 12-17, which fall into phase 4. The adapted sentence now reads: If solely incidence (i.e., cases) is minimized irrespective of YLL and mortality, then this group (sub-population 8 in Table 2) should be vaccinated before older individuals with comparably fewer contacts (sub-populations 12-17). (d) Line 118: “Interestingly however, if vaccination does not reduce virus spread (fV = 1) other than through a reduction of infections, prioritization of elderly people becomes 119 less important as the vaccine does not act as a barrier to infection among the elderly”…. This statement unclear to me. Please elaborate and discuss…. We thank the reviewer for pointing this out. We have clarified this finding with additional explanatory sentence as follows: Interestingly however, if vaccination does not reduce virus spread (fV = 1) other than through a reduction of infections, prioritization of elderly people becomes less important as the vaccine does not act as a barrier to infection among the elderly. This is evident from S3 Table when comparing the phase assignment of individuals 65 and older in the scenarios f_V=0 and f_V=1: In the latter scenario, several elderly sub-populations get vaccinated later when minimizing either deaths or cases. (e) Line 146: The following statement can be misleading: “The higher the relative contagiousness of vaccinated individuals, the higher was the influence of vaccine function on mortality; if vaccinated individuals did not cause any new infections, vaccine function had no noticeable effect on mortality”. This can be understood in a general sense: vaccination does not decrease mortality. Please reformulate to convey the sense of comparison…. We agree with the reviewer: the statement may be misleading, especially when read by a non-expert who may not understand the comparison conducted here. We rewrote the statement (and also slightly adapted the previous sentence) as follows: Deaths under the CDC allocation were highest in scenarios where vaccinated individuals were relatively more contagious and when a vaccine was less effective at preventing infections and more effective at reducing symptoms (Fig. 4B). In scenarios with a higher relative contagiousness of vaccinated individuals, vaccine function had a stronger influence on mortality. However, if vaccinated individuals were assumed to not cause any new infections, mortality was similar no matter if the vaccine solely prevented infections ($\\sigma=90\\%, \\delta=0\\%$) or solely prevented symptomatic infections among vaccinated infected individuals ($\\sigma=0\\%, \\delta=90\\%$). Attachments Attachment Submitted filename: Response to reviewers_PLOSONE.docx https://doi.org/10.1371/journal.pone.0259700.r002
25 Oct 2021 Decision Letter - Martial L Ndeffo Mbah, Editor Evaluation of the United States COVID-19 Vaccine Allocation Strategy PONE-D-21-26548R1 Dear Dr. Kadelka, 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, Martial L Ndeffo Mbah, 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: The authors have properly addressed all the requests, therefore I suggest to publish the manuscript in the present form. ****** 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 https://doi.org/10.1371/journal.pone.0259700.r003
Formally Accepted
27 Oct 2021 Acceptance Letter - Martial L Ndeffo Mbah, Editor PONE-D-21-26548R1 Evaluation of the United States COVID-19 Vaccine Allocation Strategy Dear Dr. Kadelka: 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. Martial L Ndeffo Mbah Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0259700.r004

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