Peer Review History

Original SubmissionMarch 29, 2021
Decision Letter - Martin Chtolongo Simuunza, Editor

PONE-D-21-10365

The Impact of Vaccination to Control COVID-19 Burden in the United States: A Simulation Modeling Approach

PLOS ONE

Dear Dr. Alagoz,

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Kind regards,

Martin Chtolongo Simuunza, PhD

Academic Editor

PLOS ONE

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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

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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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: No

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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

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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: This paper examines the impact of COVID-19 vaccination in the context of current nonpharmaceutical interventions in three urban jurisdictions in the United States. A strength of their agent-based model is the detailed parameterization of interactions and representation of varying levels of adherence to NPIs. Overall, the paper is well written.

1. Please update the introduction to reflect the current situation with COVID-19 vaccination in the United States.

2. In Table 1, the parameterization of vaccine effectiveness should be updated based on recent literature and data reported in real-world studies. Do you distinguish between vaccine efficacy against infection, symptomatic disease, and severe disease?

3. What is the timeline between the first and second doses? Do you account for changes in vaccine efficacy after the first and second doses, respectively?

4. The base case scenario assumes a daily vaccination capacity of 0.1% of the population per day for Dane County, Milwaukee, and NYC. Can this be supported by current vaccination roll-out data in these 3 regions? Do you anticipate this to change in the future with vaccine hesitancy?

5. Does the model account for pre-existing immunity (i.e., from previous COVID-19 infection)?

6. It is suggested in the paper that regions need to maintain a high level of adherence to NPIs to keep caseloads low. At what point in the vaccination campaign can these NPI measures be lifted successfully?

7. A number of other agent-based modelling papers have already been published regarding the population-level impact of COVID-19 vaccination in various jurisdictions (see below). Please situate your findings in the context of the existing literature.

https://doi.org/10.1093/cid/ciab079

https://doi.org/10.1016/j.vaccine.2021.03.058

Reviewer #2: The paper presents an agent-based model integrating adherence to NPIs, vaccination strategies (and possibilities) and the interactions between both of them.

The current paper presents an extension of an already existing model (COVAM), adding vaccination strategies.

A first point is that the paper is not self-content as far as the presentation of the model is concerned: the description is too short to understand what are the characteristics and behaviors of the agents. The description makes the reader question the fact that the model is really an agent-based model and not a micro-simulation model.

p4: "The objective of this study was to use our previously developed agent-based simulation model (2),"

it could be clearer to express that this previously developed model is a COVID-19 model (a lot of COVID models are adaptation of models about other diseases.

Figure s1. Progression of COVID-19 (adapted from Alagoz, et al 2020(1))

The epidemiological model has some flaws:

- There is no compartiment for asymptomatic, which is a key feature of the COVID-19

- if IM- is undetected and IM+ detected, it seems intuitive to have an arrow from IM- to IM+

- Instead of infected, infectious would more reflect what is important from an epidemiological point of view.

Methods :

Nothing is said about experimental conditions, in particular concerning the simulations launches conditions: use of HPC or personal computers ...

page9: "We ran 100 replications for each experiment" : why this number of 100 replications, how is it justified.

About adherence

"For instance, a 70% adherence level to NPIs in Dane County and Milwaukee is implemented by simply reducing the number of daily contacts from 10 per day to 3 per day per person, which slows the transmission of SARS-CoV-2."

Even if an individual has a 100% adherence level to NPIs, its daily contacts will not sink to 0... (it can be in family, it will need to buy some essential goods (foods...)).

This idea of adherence to NPIs is interesting, but its implementation seems to simplistic.

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Reviewer #1: No

Reviewer #2: No

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Revision 1
Decision Letter - Martin Chtolongo Simuunza, Editor

The Impact of Vaccination to Control COVID-19 Burden in the United States: A Simulation Modeling Approach

PONE-D-21-10365R1

Dear Dr. Alagoz,

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.

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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,

Martin Chtolongo Simuunza, PhD

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

Reviewer #2: All comments have been addressed

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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

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: 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

Reviewer #2: 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

Reviewer #2: 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)

Reviewer #2: (No Response)

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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

Reviewer #2: No

We have attached a separate point-by-point response document.

Attachments
Attachment
Submitted filename: Response to reviewers.docx
Formally Accepted
Acceptance Letter - Martin Chtolongo Simuunza, Editor

PONE-D-21-10365R1

The Impact of Vaccination to Control COVID-19 Burden in the United States: A Simulation Modeling Approach

Dear Dr. Alagoz:

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. Martin Chtolongo Simuunza

Academic Editor

PLOS ONE

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