Peer Review History
Original SubmissionApril 22, 2020 |
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PONE-D-20-11631 INFEKTA: A General Agent-based Model for Transmission of Infectious Diseases: Studying the COVID-19 Propagation in Bogotá - Colombia PLOS ONE Dear Dr. Gomez, 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 Jul 12 2020 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:
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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: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: I Don't Know ********** 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: This manuscript describes a novel agent-based model of SARS-CoV-2 transmission. The model includes public transportation, which is a feature frequently ignored in mathematical and computational models. This feature is particularly relevant for the local context of Bogotá, given the potential transmission of SARS-CoV-2 in the local public transportation system (Transmilenio). Transmission in the model occurs through interactions among individuals in different places. The places visited by each individual is based on a trajectory defined for each agent. Once infected, individuals follow a modification of the SEIR model, including seriously-infected and critically-infected individuals. The authors simulated 1001 individuals with demographic characteristics representative of Bogotá. The preliminary analyses from the authors showed that around 20% of the population would be infected within 30 days, and found that social distancing policies reduce the number of infected individuals. The model presented is interesting and the authors make an effort to include realistic interactions between individuals. However, I have some concerns about the model and the results presented. I hope my comments are useful to the authors to improve their manuscript. 1. Size of the simulations and model capacity The simulations presented in this study only include 1001 individuals. This is only a small fraction of the total population of Bogotá (8+ million). I'm concerned that this small size does not represent the density of the city. The synthetic population is geographically located according to the population density of the city, but with only 1001 individuals, the density of contacts is much lower than in reality. In this sense, the authors might be simulating a much less dense city than Bogotá. In addition, the small sample size would increase the impact of stochastic effects in the model, so that the epidemic could die out much sooner than expected.. This can explain why the authors found a similar effect of reducing social interactions by 75% than by 95%. I recommend looking into other agent-based models that don't simulate the entire population (https://www.mobs-lab.org/uploads/6/7/8/7/6787877/tracing_main_may4.pdf). Also, multiple simulations of the model could account for these stochastic effects, but the authors do not mention how many replicates were simulated with the same set of parameters. 2. Epidemiological model The transmission model might not be the appropriate for SARS-CoV-2. As I understand the model, exposed individuals are able to transmit the virus, which doesn't account for the incubation period of the virus. In addition to the incubation period, two important aspects of SARS-CoV-2 transmission should be included: asymptomatic transmission and pre-symptomatic transmission. 3. Place-specific contact rate/transmission probability It's unclear to me if the transmission rates are the same for each place. If so, this might be unrealistic. The authors should account for place-specific contact rates to determine the transmission probability. For instance, if an individual works in a workplace with 1,000 employees, would INFEKTA consider that these contacts are as relevant for transmission as household contacts are? 4. Simulation experiments The simulation experiments in this manuscript might not be enough to show the model capabilities. The current simulation experiments only take into consideration social distancing but the authors omit any specific public transportation intervention. Given that including public transportation routes is a strength of this work, the authors could perform some simulations that show the impact of changes in public transportation schedules and capacity. Current policies in Bogotá limit the capacity of transmilenio to about 35% of total capacity. The authors could explore similar strategies. Finally, it isn't clear how transmission occurs in the public transportation. Does it only happen in the terminals or bus routes? Other comments: - Abstract: "a Euclidean" should be "an Euclidean" - Abstract: What are the main results of this study? - Line 17-18. Try to avoid using "predicting", use estimating or projecting instead - Lines 24-25. Should "social separation" be "social distancing"? - Lines 26 - 77. This section might be unnecessarily long, and could be a part of the introduction. More importantly, I suggest that the authors elaborate more on the recent agent-based models available in the literature for COVID-19. It would be helpful to have more context on the current modeling approaches (Examples: Ferguson et al., or Vespigniani et al.) and how INFEKTA compares to those models. - Lines 99-102. "No home is neighbor to any other home". Does this mean that neighborhood interactions among individuals only occur at public transportation stations? - Line 145. Please explain Figure 1 with more detail. - Methods: It isn't clear to me if the parameters for transmission are fixed parameters or drawn from a distribution. - Methods: It isn't clear to me which processes are random and which are deterministic in the model. - Methods: Please explain in more detail how the synthetic population was created to match demographic characteristics of Bogotá. - Lines 188-232: How do the authors account for the difference in the 1001 people in the simulation and the actual population of Bogotá? If the entire city is being simulated but only 1001 people are modeled, how does this affect the transmission dynamics? Is there any factor to account for the difference in synthetic and real density? - Lines: 286-290. This could be caused by the small sample size. Stochastic effects can make a big difference with only 1001 people simulated. - Discussion: How does this model compare to other ABMs around the world? Reviewer #2: 1. In abstract, the sentence “In this paper, a general agent-based model, called…”, I am not sure what authors mean by a general agent-based model. The word general sounds like a specific type of ABM. I suggest to explain what the word “general” means in this context, and if the ABM is a regular ABM, this word in unnecessary. 2. I suggest that authors add at least one more line in the abstract where one central or maybe the most important result of the paper is presented. I believe that usually this attracts reader attention. 3. In introduction, the sentence (line 10) “Complex systems are computational approaches that make use of computer-based algorithms to model dynamic interactions between individuals agents…” is not accurate. Please, revise the complex systems concept. Actually, this sentence make an inversion between complex systems and computer-based algorithms. Complex systems may be simulated by using computer algorithms, but the concept of such systems are wider than the one expressed in this sentence. 4. I think that the subsection “Complex Systems Approaches for Epidemic Models” (line 26) would make more sense if it is locate after the subsection “Compartmental Model” (line 37). Thus, the new sequence would be “Compartmental Model” and after this subsection, “Complex Systems Approaches for Epidemic Models”. My argument is that initially authors should explain what compartmental models are and the limitations they might have. After that, an introduction about complex systems approach an then, the ABM subsection. 5. First paragraph of the subsection “Agent-based models for infectious disease” is fine, although I think authors could add a comment about that agents in an ABM model may take decisions based on some system conditions or rules. 6. Lines 67 to 70 are repeating what was already mentioned about ABMs and complex system, then I suggest, as these lines a redundant, they could be deleted. 7. The sentence in lines 73 to 75 are not very clear to me. Is this what authors meant: In this way, each virtual individual includes its health state, as implemented in a SEIR model, which is fundamental for the infectious disease transmission? 8. In Section “INFEKTA Agent-Based Model”, for the sake of simplicity, the first paragraph should be reduced to “Our agent-based model of infectious disease propagation, called INFEKTA, consists of five-layer components:”. The remaining part of line 80 until line 85 may be delete because each one of the model layers are explained right after the colon. Therefore, I think that the text would benefit of clarity if each layer does not have subsection, maybe items or subitens. For instance, the layer “Space” should explain “Place (Node)” and “Neighbor (Edge)” as part of the same text the item “Space”. The same idea may be applied to explanation of the other remaining layers. 9. Lines 87 to 90: important concepts of the model are presented in these lines. Part of them are between parentheses, so I suggest that they be place between commas, because they are fundamental to understand the concept that is being exposed. 10. Neighbor (Edge), line 98: concept is simple but the relations (neighborhood) among them are not very clear in the explanation. Authors may consider two options: re-write the sentence or add a simple figure representing each concept and the relations among them. 11. Line 100, the footnote: replace "in" by "In". 12. Line 119. What is “Going hour”? There is no definition for it in the text. 13. Line 135. In the case of covid-19, as literally everybody is susceptible to the SARS-Cov-2 virus, the health state “Immune (M)” only makes sense when the individual is recovered from the disease. However, the “Recovered (R)” health state is also defined in the model. Then, my question is: what is the difference between the two health states? Besides, in line 142, authors say “INFEKTA introduces both the M state since some individuals are naturally immune”. In the literature, one can find that, if so, only a few persons have some partial immunity against SARS-Cov (not SARS-Cov-2), however, this is not a lifetime imunnity and this outbreak happened in the early 2000’s. Moreover, the amount of people infected with SARS-Cov is so small and geographically restricted that does not justify to model a pandemic caused by SARS-Cov-2 considering that some individuals have any prior immunity. Then, this part of the text has to be re-written. Figure 1 shows clearly the immunity is acquired only after the individual has recovered from the infection: this is the correct dynamics of covid-19 outbreak and, as recovered individuals have acquired immunity immune, a new compartment called “M” is not necessary. In addition, in Fig.1, there is a line from R compartment to S compartment, meaning that recovered individuals become susceptible again. So far, in the literature about covid-19 pandemic there is no evidence that recovered individuals become susceptible again. Thus, this fact implies that this model has to be considered incorrect and for this reason, until this correction is made, I suggest the paper is rejected. ********** 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: Guido Camargo España 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. |
Revision 1 |
PONE-D-20-11631R1 INFEKTA: An Agent-based Model for Transmission of Infectious Diseases: Studying the COVID-19 Propagation in Bogotá - Colombia PLOS ONE Dear Dr. Gomez, 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. ACADEMIC EDITOR: Please address the small changes suggested by Reviewer 1. Please submit your revised manuscript by Jan 23 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. 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:
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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Rebecca Lee Smith Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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: (No Response) Reviewer #2: 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 Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A 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: The authors addressed most of my comments in an acceptable manner. Below some additional comments. First, I apologize for my misguided comment on `a Eucledian`. It is indeed spelled `a Eucledian`, not `an Eucledian`. - There is still an issue with my first comment regarding the stochasticity nature of the model and the population size. In terms of the stochasticity, the authors only report the mean of their results, do not include any uncertainty. For the population size, I understand the need for simplification in the population size, but the authors should at least add in the discussion what impact does this underestimation have in their results. For instance, transmilenio buses or stations would be less crowded than expected, given that there are fewer people in the model. In general, the authors should add a section in the discussion listing the model limitations. - The authors added a couple of other models in their introduction, which I appreciate. I don't agree that this model differentiates in having a complex network of places and population density. Several of the agent-based models that have been available for a long time to simulate COVID-19 include realistic representations of human activities and their population demographic characteristics. Including public transportation might be a more unique characteristic of this model. Also, there are many more than two abm for COVID-19, and have been released before this manuscript was under review. - For future reviews. Please add the line numbers where the changes have been made. It is difficult to follow the responses without the lines where the changes were made. - Abstract: `not so hard` -> please use specific and descriptive words. - Line 306-309. the statement "indicate that INFEKTA may be a valuable asset for researchers and public health decision-makers for projecting fugure scenarios when applying social distancing policy rules" is not supported by their results. 1. The authors do not contrast their simulations to any data in the manuscript to calibrate model parameters, 2. The authors do not make any projections and contrast them with epidemiological data in Bogotá. If the model is not validated with data, how can it be used to project future scenarios? I think the model could be used to explore scenarios, but not to project or predict. Reviewer #2: As the authors have addressed all the suggestions and requested corrections, I think the paper is suitable to be published. ********** 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: Yes: Aquino L. Espindola [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. |
Revision 2 |
INFEKTA: An Agent-based Model for Transmission of Infectious Diseases: The COVID-19 case in Bogotá, Colombia PONE-D-20-11631R2 Dear Dr. Gomez, 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, Rebecca Lee Smith, D.V.M., M.S., Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
Formally Accepted |
PONE-D-20-11631R2 INFEKTA - An Agent-based Model for Transmission of Infectious Diseases: The COVID-19 case in Bogotá, Colombia Dear Dr. Gomez: 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. Rebecca Lee Smith Academic Editor PLOS ONE |
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