PCLM-D-23-00139

Evaluating the effect of land use/land cover, and climate on malaria incidence in the Ecuadorian Amazon.

PLOS Climate

Dear Dr. Araujo Navas,

Thank you for submitting your manuscript to PLOS Climate. After careful consideration, we feel that it has merit but does not fully meet PLOS Climate’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 Oct 06 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 climate@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pclm/ 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 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'.

Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

We look forward to receiving your revised manuscript.

Kind regards,

Ka Chun Chong

Academic Editor

PLOS Climate

Journal Requirements:

Additional Editor Comments (if provided):

Please address well to the comments.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Does this manuscript meet PLOS Climate’s publication criteria? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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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 (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. 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 Climate 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: No

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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 authors present an interesting topic on evaluating the effect of land 1 use/land cover, and climate on

malaria incidence in the Ecuadorian Amazon. This research is current, timely, relevant in areas where malaria prevalence is increasing on yearly basis.

Few points to be considered:

1. Line 123 - Did you considered only surface temperature or you looked at air temperature as well?

2. did you look at rainfall data because this is one of the characteristics that affect the distribution of vectors

3. Line 123-124- "surface runoff" how do you mean?

Line 132 - LULC types was downloaded from the ministry database. Did you you do ground truth for confirmation? Meanwhile in Lines 178-179 - there was a collinearity between agriculture and forest, did you suspect lack of ground truth as the cause?

Line 133 - Landsat was used but we did know which of he Landsat? More so, did you use ETM or ETM because part of the years used, more advanced Landsat has been introduced

Line 136 - Is urban areas the same as settlement?

Line 141 - The use of the variable "malaria incidence" seems to be at variance with the actual meaning in this context. Same for lines 148-149

Line 204; Kindly remove ethical approval from your sentence because the later part showed that you obtained ethical clearance for this project.

Line 242-250- Please, kindly show us the difference between "incidence" and "prevalence"

Lines 251 and 264 - I find it difficult to follow tables 2 & 3

Figure 1 - I can't find symbol for census areas

Figure 2 - Plasmodium species were not italicized

Figure 3 - Some labels are not clear enough.

Reviewer #2: General comment:

The manuscript presents malaria incidence data and their cross correlation with the land use/Land cover in the Ecuadorian Amazon. Despite several shortcomings that need to be addressed by the authors, the information is very relevant to the reader and deserves publication in the PloS Climate.

Specific comments:

1. Study area and malaria incidence data:

Line 108: “Microscopy was used as the primary method of diagnosis (15)”. For this study, please describe other type of dianostic tests that were used to define malaria case, such as immunochromatographic test or rapid diagnostic test or clinical diagnosis. This information will help increase the quality of the malaria data.

Line 109: What do you mean with “epiweek level”. Please replace the term with a more common/standard term. Does it mean weekly incidence?.

2. Data preparation

Line 142: delete “plasmodia”.

Please clarify the spatio-temporal unit of malaria incidence. Number of malaria cases stratified by species per 1000 population per Canton. Does the “Canton” also represent different LU/LC?.

3. Results

Line 241: Use Plasmoium vivax instead of Plasmodia Vivax

Line 254: Use Plasmodium falciparum instead of Plasmodia Falciparum.

The vast majority of malaria cases were P. vivax. How are the species (P. vivax and P. falciparum) distributed across different spatiotemporal setting?.

4. Discussion

Line 280 replace “plasmodia with P. falciparum and P. vivax

Study limitation:

The authors concluded that “ Increases in shrub vegetation and forest ARC, temperature, and terrestrial water content are consistently associated with decreases in both plasmodia. In contrast, increases in precipitation show an opposite relationship with malaria incidence”. I think the authors should discus the above conclusion in a more systematic way and supported with other previous documented results, as this is actually the “result” of this study.

The authors should also discuss the limitation faced by this study, particularly to properly record the dynamic change of the LU/LC across the study period

Reviewer #3: Overall, the paper presents a valuable investigation into the effects of climate and LULC on malaria incidence in the Ecuadorian Amazon. With some organizational adjustments and clarifications, the manuscript could become even more accessible and impactful for readers in the field. Simplify complex sentences and technical language where possible to improve readability. Improve grammatical constructions across the paper.

1.Title:

The title could be improved for clarity and conciseness. Consider revising it to "Impact of Climate and Land Use Changes on Malaria Incidence in the Ecuadorian Amazon" or a similar version that clearly conveys the main focus of the study.

2. Abstract Clarity:

The abstract provides a clear overview of the study's focus and methodology. However, it could be more concise by eliminating some unnecessary details, such as specific statistics that are better suited for the main body of the paper. Try to condense the main points while maintaining clarity. Additionally, consider rephrasing complex sentences to improve readability.

See suggestion for a guide:

Background: Malaria transmission is influenced by climate and land use/land cover change (LULC). This study examines the impact of climate and LULC on malaria risk in the Ecuadorian Amazon.

Methods: Weekly malaria surveillance data (2008-2019) from Ecuador's Ministry of Public Health were combined with hydrometeorological and LULC data. Cross-correlation analyses identified time lags, and a Bayesian spatio-temporal model estimated annual LULC rates of change (ARC) by census block. Bayesian models assessed effects on malaria species incidence.

Results: ARC for five land cover classes (forest, agriculture, urban, shrub vegetation, water) ranged from -1% to 4%, with agriculture increasing across areas. Forest and shrub vegetation ARC were significantly associated with both P. vivax and P. falciparum incidence. Temperature and terrestrial water content showed consistent negative relationships with both species. Precipitation had opposing effects on P. vivax (decrease) and P. falciparum (increase) incidence.

Conclusions: Shrubs and forest expansion, increased temperature, and terrestrial water content reduced malaria incidence, while increased precipitation had varying effects. Relationships between malaria, LULC, and climate are complex, influencing risk profiles. These findings aid decision-making and guide further research in the region.

Keywords: malaria incidence, climate, land use/land cover, Bayesian modeling.

3. Introduction:

The paper provides a comprehensive introduction to the context of malaria in the Ecuadorian Amazon, discussing historical trends, vector species, prevalent pathogens, and environmental factors. However, some parts of the introduction are overly detailed and could be streamlined for clarity. It lacks a succinct problem statement that clearly states the research gap and the specific objectives of the study.

Consider condensing some of the historical and background information to emphasize the research gap and objectives.

In line 77, how does precipitation facilitate human movement?

Materials and Methods:

This section is detailed and informative, explaining the study area, data sources, and analytical methods used. Explicitly address limitations and potential sources of bias in the study design.

In line 122: state the hypothesis and reference S1 Table

Results:

The results section is detailed and comprehensive, presenting the findings of the study in a clear manner. Simplify complex sentences and technical language where possible to improve readability.

Discussion:

The discussion section provides a thorough interpretation of the findings in relation to existing literature. However, it could be organized more logically by discussing the results in the context of the research questions stated earlier in the introduction. This would help to address the research objectives and discuss the implications of the findings more directly.

Discuss potential mechanisms behind the observed associations and address limitations more explicitly. Elaborate the potential biological and ecological mechanisms that could explain the observed relationships between climate, LULC, and malaria incidence.

Answer the question, why might temperature and terrestrial water content have consistent negative effects on both species, while precipitation has different effects? Explain why certain variables (e.g., precipitation) had opposing effects on different malaria species and discuss potential ecological mechanisms behind these results.

Discuss the practical implications of the findings for malaria control and prevention strategies in the Ecuadorian Amazon. How can decision-makers use this information to improve interventions?

In line 278, what do you mean by, “… but not in simple ways”?

Conclusion:

Enhance the conclusion by restating main findings and their significance. Clearly state contributions and how findings advance understanding of malaria dynamics in the Ecuadorian Amazon. Suggest potential policy implications or future research directions based on outcomes.

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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.

Do you want your identity to be public for this peer review? If you choose “no”, your identity will remain anonymous but your review may still be made public.

For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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[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.

PCLM-D-23-00139R1

Impact of climate and land use/land cover changes on malaria incidence in the Ecuadorian Amazon

PLOS Climate

Dear Dr. Araujo Navas,

Thank you for submitting your manuscript to PLOS Climate. After careful consideration, we feel that it has merit but does not fully meet PLOS Climate’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 Dec 15 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 climate@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pclm/ 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 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'.

Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

We look forward to receiving your revised manuscript.

Kind regards,

Ka Chun Chong

Academic Editor

PLOS Climate

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.

Additional Editor Comments (if provided):

Please address the minor comments.

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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 #2: All comments have been addressed

Reviewer #3: All comments have been addressed

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2. Does this manuscript meet PLOS Climate’s publication criteria? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #2: Yes

Reviewer #3: Partly

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

Reviewer #2: I don't know

Reviewer #3: N/A

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4. Have the authors made all data underlying the findings in their manuscript fully available (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. 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 #2: Yes

Reviewer #3: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS Climate 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 #2: Yes

Reviewer #3: 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 #2: Review on Manuscript Plos Climate:

Title: Impact of climate and land use/land cover changes on malaria incidence in the Ecuadorian Amazon

Manuscript Number: PCLM-D-23-00139R1

General Comment: The authors have properly addressed points raised the reviewers except for several statement that still needs clarification. Typhos were also noted and corrected accordingly.

Specific comment:

Lines 99-102 Microscopy was used as the primary diagnostic method, nevertheless, rapid

diagnosis tests were also used in health centers where these were available (15).

Diagnosis methods were based on clinical and epidemiological criteria. Clinical

criteria included fever, shaking chills, sweating, headache, sickness, and dizziness.

Comment: The use of clinical diagnosis in this study should be further clarified by the author as to what extent it is used.

Line 256: Plasmodium Vivax should be written Plasmodium vivax

Line 268 Plasmodium Falciparum should be written as Plasmodium falciparum

Reviewer #3: The authors have made notable improvements in this latest version of the manuscript. However, there is room for further enhancement through minor revisions. Below are specific suggestions for the authors to consider:

1. Clarity in Temperature and Terrestrial Water Content Discussion:

• The discussion on temperature and terrestrial water content is crucial but could benefit from simplification for a wider readership. Consider using more accessible language and clearer explanations to enhance overall comprehension.

2. Data Limitations:

• Acknowledge the limitations associated with the absence of data on interventions and socio-economic factors. Strengthen the study by discussing the potential impact of these limitations on result interpretation. Also, highlight areas for future research that could address these gaps.

3. Maps Legends:

• Refine the legends to create a mutually exclusive scale (<100, 100–500, 600–1000, 1001–2000, etc.) instead of the current mutually inclusive scale (100-500, 500-1000, 1000-2000). Additionally, use an en-dash (–) for number or year ranges, avoiding hyphens (‐) for better clarity (e.g., (-3)–(‐2), (-1)–(0), 1–2, or 2001–2008).

4. Consistency in Terminology:

• Ensure consistency in the use of terminology throughout the paper. Opt for either "P.vivax" or "Plasmodium vivax" consistently to enhance clarity and readability.

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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.

Do you want your identity to be public for this peer review? If you choose “no”, your identity will remain anonymous but your review may still be made public.

For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #2: No

Reviewer #3: No

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[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.

Impact of climate and land use/land cover changes on malaria incidence in the Ecuadorian Amazon

PCLM-D-23-00139R2

Dear Mrs. Araujo Navas,

We are pleased to inform you that your manuscript 'Impact of climate and land use/land cover changes on malaria incidence in the Ecuadorian Amazon' has been provisionally accepted for publication in PLOS Climate.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow-up email from a member of our team. 

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

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 climate@plos.org.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Climate.

Best regards,

Ka Chun Chong

Academic Editor

PLOS Climate

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The authors have addressed the comments well.

Reviewer Comments (if any, and for reference):