PONE-D-22-35076Chikungunya long lasting immunity in the Mayotte population will not be enough to prevent future outbreaks: A seroprevalence study, 2019.PLOS ONE

Dear Dr. Ortu,

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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: Partly

Reviewer #2: Yes

Reviewer #3: Partly

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

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: 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: No

Reviewer #2: Yes

Reviewer #3: Yes

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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

Reviewer #3: 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: The study investigated the susceptibility level of CHIKV in human population in Mayotte using the serological data randomly sampled in the region. They concluded that the immunity in CHIKV is long-lasting and the current immunity from the previous outbreak is not enough to protect from future outbreaks. I found this conclusion a bit inaccurate and may need to revise some discussion points. Some of the analyses in the manuscript should also be revised.

The previous outbreak in Mayotte was in 2005-2006 and the serological data from 2019 was investigated in this study. Unfortunately, the serological data is missing age group < 15, which contains crucial information to know if there are any additional outbreaks in the region 15 years since 2005. The authors were aware of this problem and already discussed it. Besides no report of CHIKV transmission in the region since 2005, by observing that the seroprevalence in the population remains the same compared to the previous study across all age groups, we have a stronger evidence that there were no activity of the virus since 2005. This point should be added to the discussion section.

I suggest the authors should assess for multicollinearity using VIF rather than just collinearity. I also wonder why the threshold of 0.5 was chosen for the pairwise correlation to reduce the number of variables. Why not 0.7 or any other numbers? I suggest the authors attempt to reduce the dimension of the variables by other means such as stepwise regresion.

The results from the univariate analysis should be summarized or discussed somewhere in the manuscript.

I also wonder why the authors perform the analyses on the three models with different fixed set of covariates. Some kind of variables selection procedure here may make the method more robust.

“Based on an estimated basic reproduction number of 2.8 reported for areas where Aedes albopticus is the primary vector (29), roughly 65-70% of the population should be immune to CHIKV to avoid an epidemic; therefore, the possibility of future epidemics in Mayotte cannot be excluded.” I found this point to be problematic. The 65-70% figure is derived from the R0 of 2.8 assuming that the population is homogenous. This in reality is not true for aborviruses, where their transmission dynamic are highly heterogenous. Given the heteogenousity, the herd immunity threshold can be much lower than 65-70%, hence current immunity level in the population maybe enough to prevent epidemic to happen in the near future. Furthermore, the authors seems to ignore the uncertainty of the R0 estimation, which lead to the uncertainty in the herd immunity threshold as well. I also found the conclusion for this point is weak, since in the future, as the susceptible pool is increasing over time from the newborns, it is inevitable that “the possibility of future epidemics in Mayotte cannot be excluded.”

“Knowledge of other mosquito-borne diseases such as malaria, appeared to be positively associated with the presence of CHIKV antibodies. This association could reflect a heightened awareness of mosquito-borne infectious diseases among individuals affected by malaria or chikungunya.” I failed to see the authors’ logic of this point. I believe there is a potential confounder here, knowledge of malaria and presence of CHIKV antibodies are both correlated with high risk of arboviruses infection.

The lines in the manuscript should be numbered.

Reviewer #2: Dear authors,

Excellent work conducting this work and conveying key information about a neglected disease. Please see some specific comments below:

Is it possible to add a map illustrating the different regions of Mayotte and their respective seroprevalence? A figure would be helpful for readers unfamiliar with the island when discussing the geographic findings of the study.

Introduction, 2nd paragraph, line 4, remove “has” in “where presumably CHIKV has originated”

Introduction, final paragraph, line 4, change “insight of” to “insight into”

Setting, paragraph 1, line 3, change “is holding” to “holds”

Study design, paragraph 1, line 1, change “consists in” to “consists of”

Data collection, paragraph 2, line 7, change “Besides,” to “Additionally,”

Determinants of anti-CHIKV IgG seropositivity, paragraph 3, line 1, change “being resident either in Mamoudzou” to “residing in either Mamoudzou”

Determinants of anti-CHIKV IgG seropositivity, paragraph 3, line 2, remove “the” in “associated with the higher”

Determinants of anti-CHIKV IgG seropositivity, paragraph 3, line 3, change “being resident” to “residing”

Determinants of anti-CHIKV IgG seropositivity, paragraph 4, line 3, change “toilette” to “toilet”

Discussion, paragraph 2 - “therefore we should add this population to the group of susceptible individuals.” Is it possible to provide a quantitative estimate of this value? Ie. if you assume all members of the population below 15 are seronegative and calculate a new percentage including these individuals, by how much does the 65% susceptibility estimate increase?

Reviewer #3: Ortu et al. performed a serosurvey and questionnaire in Mayotte, where a CHIKV outbreak took place in 2006. The authors performed IgG ELISA to determine previous CHIKV exposure and applied questionnaires exploring socio-demographic factors and knowledge of mosquito-borne diseases. Although the part of the study looking at CHIKV IgG could be substantially expanded upon, by doing quantitative ELISA, neutralization assays, and T-cell assays to assess the population immunity, the igG data presented here will be a valuable addition to the literature for understanding CHIKV present and future outbreaks.

Major comments:

1.The title of the manuscript claims that the current immunity will not be enough to prevent future outbreaks. This claim is based on a report that estimates that at least 65% of the population would need to be immune to prevent future epidemics. However, in this paper the authors only perform a positive/negative IgG, and do not assess other parts of the immune system that could give partial immunity to CHIKV such as T-cells, and proportion of neutralizing antibodies, cross-neutralizing antibodies from similar alphaviruses. Therefore, the authors should consider changing the title to reflect their data accurately.

2. The authors stored the sera at -20C. Please add how long the sera was stored for. How long are IgGs stable for at -20C?

3. The references need to be improved on several occasions:

•The authors cite a manuscript in preparation; this is highly unusual, and I strongly suggest removing that citation. The details on the methodology should be included in this manuscript, in the methods or supplemental files, or a published source could be cited.

•References 15-17 look like they need more information, is that citing a book chapter?

•While citing reputable websites is acceptable, the authors cite many websites. I would suggest reducing the number of website citations wherever possible and adding the date accessed for any that will be kept. Links to websites tend to break with time and no longer be accessible.

•Reference 31 is all in caps, while the others are not.

4. More details are needed regarding the ELISA. Please clarify if the ELISA is for total IgG, IgG-1 or other. Please specify how the ELISA threshold was chosen. If it was recommended by a manufacturer or based on previous experience or statistical method.

5. Since the authors are working with human blood from a region that may have CHIKV present, the authors should specify how the samples were handled, ie/ level of containment, any heat inactivation done, if anything was done in case blood was collected from a patient with CHIKV symptoms. Although the samples were not known to contain CHIKV, this virus is typically BSL-3 in Europe and the US.

Minor comments:

1. Would it be possible for the authors to use a known sample as standard curve to quantify the IgGs?

2. The "attitudes to mosquito-borne disease prevention" data is not showing on table 2, I think it was cut off.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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PONE-D-22-35076R1Long lasting anti-IgG chikungunya seropositivity in the Mayotte population will not be enough to prevent future outbreaks: A seroprevalence study, 2019.PLOS ONE

Dear Dr. Ortu,

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 remaining queries and suggestions by one of the reviewers. 

==============================

Please submit your revised manuscript by May 26 2023 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,

Joel Mossong, PhD

Academic Editor

PLOS ONE

Journal Requirements:

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.

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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

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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: Partly

Reviewer #2: Yes

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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

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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 acknowledge your general feedback – thank you. We mentioned the evidence of not circulation of CHIKV in Mayotte in the discussion - please see lines 288-292."

No report does not mean no circulation of the virus. Please add the point I have made in my previous comment for the discussion. The positive proportion remains the same compared to the previous study in 2006 means that there are no or minimal transmission of the virus since then. If there was an outbreak recently, the positive proportion must be way higher than the previous one. This is a stronger argument for the no circulation in the region point and should be added to the discussion.

"By using Spearman test we did consider multicollinearity rather than collinearity, as we checked the correlation byrunning the Spearman test with all the variables at once (although the output shows all possible combinations of correlation among each 2 variables). We did not opt for using the VIF command"

No pair-wise co-linearity does not exclude the possibility of multicolinearity.

I do not get the difficulty to calculate VIF since the authors only need to calculate it based on the variables

"Based on some reading on Spearman test, the use of it, and the interpretation of thresholds - see for instance these:

https://geographyfieldwork.com/SpearmansRankCalculator.html,

https://statistics.laerd.com/stata-tutorials/spearmans-correlation-using-stata.php

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3576830/ we opted for choosing 0.5 as the threshold. The range between 0.5 and 0.7 is generally associated to moderate correlation. As we did not want to have correlation as a factor that would somehow impact the analysis, 0.5 seemed to be an appropriate and conservative threshold to use (alongside a significant P value)."

Please add these reference to the manuscript to explain why you choose the number.

"We could not conduct an automated stepwise logistic regression using the stepwise command in STATA as the svy prefix command is not compatible with it. However, we did stepwise regression “manually”, specifically we used a backward stepwise process with the commands svy,:poisson and test."

I am not familiar with STATA syntax so I cannot get what the authors trying to say here. Please use statistical terms to explain your reasoning.

Reviewer #2: Thank you for addressing the comments submitted by the reviewers. All of my comments and questions are now resolved.

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Reviewer #1: No

Reviewer #2: No

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Long lasting anti-IgG chikungunya seropositivity in the Mayotte population will not be enough to prevent future outbreaks: A seroprevalence study, 2019.

PONE-D-22-35076R2

Dear Dr. Ortu,

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,

Joel Mossong, 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

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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

**********

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)

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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

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