https://orcid.org/0000-0003-1801-7938
Peer Review History
| Original SubmissionJuly 21, 2022 |
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PGPH-D-22-01209 Antiretroviral treatment failure and associated factors among people living with HIV on therapy in Homa Bay, Kenya: A retrospective study PLOS Global Public Health Dear Dr. Masaba, Thank you for submitting your manuscript to PLOS Global Public Health. After careful consideration, we feel that it has merit but does not fully meet PLOS Global Public Health’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 09 2022 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 globalpubhealth@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pgph/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised 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, Sanghyuk S Shin Academic Editor PLOS Global Public Health Journal Requirements: 1. Please amend your detailed Financial Disclosure statement. This is published with the article. It must therefore be completed in full sentences and contain the exact wording you wish to be published. a. Please clarify all sources of funding (financial or material support) for your study. List the grants (with grant number) or organizations (with url) that supported your study, including funding received from your institution. b. State the initials, alongside each funding source, of each author to receive each grant. c. State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” d. If any authors received a salary from any of your funders, please state which authors and which funders. 2. We have noticed that you have uploaded Supporting Information files, but you have not included a list of legends. Please add a full list of legends for your Supporting Information files after the references list. 3. In the online submission form, you indicated that "The datasets generated and/or analyzed during the current study are presented in the figures and tables in the manuscript. The analytic datasets are available from the corresponding author on request.". All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons by return email and your exemption request will be escalated to the editor for approval. Your exemption request will be handled independently and will not hold up the peer review process, but will need to be resolved should your manuscript be accepted for publication. One of the Editorial team will then be in touch if there are any issues. Additional Editor Comments (if provided): While the manuscript is clearly written, there are a few critical flaws in statistical analysis that should be addressed. - The analysis does not take into account loss-to-follow-up (i.e. right censoring). Participant data were examined during a 4 month period (Sep 2020 – January 2021). Participants who started ART closer to the end of data collection would, therefore, have lower opportunity for VTF. This could lead to significant bias in classification of suspected TF and, thereby, bias the estimated associations of predictors. Please consider redoing the analysis to account for this bias, such as with time-to-event outcome methods. - The definition of VTF is actually those with confirmed elevated VL after EAC. The authors should justify why this outcome is meaningful. It seems that the conservative outcome classification would be to count everyone with suspected TF as VTF unless they have confirmed viral suppression at the post-EAC measure. If the goal is to identify predictors of VTF among those who receive EAC, then the denominator for that analysis should be 280 people who received EAC. Minor comments - In the Introduction or the Methods, the authors should describe what EAC entails. - Line 104. Please justify why the study included only those who were on treatment for over 6 months. - Line 104. Were all patients who were in the database with treatment over 6 months included in the sample? Please state if other inclusion or exclusion criteria were used to create your sample. - Line 109. While the timing of the data collection is reported, the range of dates for the retrospective data included in the sample is unclear. Please report the distribution of data with respect to treatment start dates. - Line 124. Please justify why VTF was defined based on VL measurements after 3 months of EAC. - Please report the number of people who had no VL measurements after 3 months of EAC classified. How were these handled in the analysis? - Lines 160-162. I found the % advanced disease reporting confusing. It is reported as 30%in line 160 and then 24.9% in line 163. Is this because the first number included WHO stage III/IV? Or because the second number excluded missing CD4? I suggest deciding on one way to present the % of advanced immune suppression and simply presenting that % only. - Line 174. The VTF rates are different than Table 3. Please make them consistent. - What was the distribution of time to VTF from EAC? - Table 2 contains the same data as Table 3 Column 4, except in column percent vs. row percent. Suggest deleting Table 2. - Line 221. The term “predictor” is used, but some of the variables include those that are likely to be the result of VTF, not antecedent predictors (e.g. CD4 <200 cells/ml). Please justify the inclusion of each variable as “predictor” in the final multivariable model from a conceptual perspective, while avoiding over-adjustment bias. (See Schisterman EF, Cole SR, Platt RW. Overadjustment Bias and Unnecessary Adjustment in Epidemiologic Studies: Epidemiology. 2009 Jul;20(4):488–95.) - Discussion. When providing context with prior studies, please explain how those studies defined VTF and whether they are comparable to the definition used in this manuscript. - Line 254. Please explain the usefulness of noting the association between higher VLs and VTF, since VTF is defined by high VLs. - Lines 267-268. I don’t believe EAC completion was presented in Results. Please include these data in the Results and use the Discussion to explain the context and implications of those results. - Lines 274-275. Please note that low CD4 counts could be the result of the VTF, not the cause of it. Please explain whether the study design allowed for the conclusions that low CD4 may have a causal association (i.e. “predictor”) with VTF. [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 Global Public Health’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 ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No ********** 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 ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS Global Public Health 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 ********** 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: Title “Antiretroviral treatment failure and associated factors among people living with HIV on therapy in Home Bay, Kenya : A retrospective study” General comments I would like to congratulate the authors for the much efforts made to produce this manuscript on “Antiretroviral treatment failure and associated factors among people living with HIV on therapy in Home Bay, Kenya: A retrospective study”. The authors made an attempt to answer the research question at satisfactory level, use the appropriate study design, presents the results and discuss the findings in light of the current literature. The authors have done a very good study. The aim of the study is clear. However, the manuscript requires minor revisions, which the authors need to address before publication. 1. Abstract Line 24: Kindly state which region are referring to. Line 36-37: Be consistent in your reporting. Kindly refer to line 35 (reporting proportion with corresponding 95% CIs). Consider removing these 95% CI relative to proportions given they do not read well. Line 38-40: It is not clear when these CD4 counts were measured. I guess these are CD4 counts at ART-initiation. If so then explicitly state (Patients who initiated ART with CD4 counts < 200 cells/mL were 2.41 times). In addition, add their corresponding 95% CIs as the reader needs to assess the level of significance and the direction of the association. Line 44: I fail to understand this part of your conclusion. In fact, HIV program implementers and Health care workers should focus on PLHIV with these characteristics in order to prevent and for early identification of ART treatment failure. 2. Background Line 48-50: Kindly verify these statistics. These are estimates are for 2020 and the reporting time is mixed up. Updates these statistics with 2021. Kindly see the link below: https://www.unaids.org/en/resources/fact-sheet Line 52: These figures are obsolete and outdated, kindly update these using the link provided in the comment above. Line 83-85: While the second part of the study aim is clear, and it has been adequately addressed throughout this paper. However, I have substantial concern regarding the following: “To better describe the HIV treatment cascade”. This was not addressed in this study. 3. Methods Line 88-89: Provide further details on the study design, especially on the direction of inquiry. Line 106-107: Is this a desired sample size based on sample size calculation or a sample size chosen arbitrarily (conveniently) based on resource and time. Kindly clarify Line 110-111: It is important to provide further details on how the random systematic sampling was conducted leading to a selection of patients included in the analysis. A single sentence will suffice Line 129-131: Your primary outcome is time-to-event data, reason why Kaplan-Meier method was used to estimate the probabilities of VTF. However, using logistic regression to identify factors associated with VTF is inappropriate for time-to-event data, given logistic regression provides biased estimates when dealing with time-to-event data. To identify factors associated with VTF, Cox-regression methods also known as proportional hazards regression is the suitable/adequate method for the type of data. Kindly re-run these models using Cox-regression methods. 4. Results Line 147-148: I am not knowledgeable of the of Kenyan context, do you mean individuals aged 0-14 were married? Line 161: Which method did you use to assess advanced HIV disease ( CD4 count or WHO staging system) ? Looking at table 1, 30% of patients had AHD and this is based on CD4 count. If this is the case, then delete WHO stage III and IV in the sentence. Line 178: This is not good practice for reporting, DO NOT report mean with 95% confidence intervals , instead report: 1. Mean with standard deviation (SD). 2. Median with IQR (as you have been reporting) On the lighter note, generally, time-to-event data are skewed or asymmetrical (not all the time), kindly check the distribution of your data before reporting the mean time to VTF, otherwise use median time to VTF. Line 220: Refer to my comment in line 129-131. The whole section will change in terms of interpreting findings. I am not expecting substantive changes in the overall results or key findings. There is a sizable number of papers to why Cox proportional hazards models are more suitable instead logistic regression models in when dealing with time-to-event data. https://www.nature.com/articles/ejhg200859 3. Discussion Line 237-239: This is critical part of the discussion section as it summarises key findings of the paper. Kindly add VTF was significantly higher among PLHIV who stared ART with CD4 <200 cells/mL. Line 247: Change population observed to the "populations studied". Furthermore, the variation observed between your study and Kadima et al. could be partly explained by differences in age cut-off for children. Line 258-259: Additional innovative strategies to address sub-optimal adherence to ART among adolescents would be establishment of youth-targeted services, exclusively to youth. https://onlinelibrary.wiley.com/doi/full/10.1002/jia2.25854 Line 269: I suggest adding a more recent evidence from South Africa. https://onlinelibrary.wiley.com/doi/full/10.1002/jia2.25854 Line 298: What is the possible impact of missing CD4 count data on main findings? Missing data often leads to under or over-estimation (could bias your estimates) of the measures of effects (in the context of your study, this could lead an over or under-estimation of the association between CD4 count and VTF) Line 303-304: Consider to add another strength: "Our study was conducted under programmatic conditions (real-world conditions) using routine medical records at public health facilities, demonstrating the burden of VTF in real-world conditions, therefore, maximizing generalizability". ********** 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: Yes: Marcel Kanyinda Kitenge ********** [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 |
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PGPH-D-22-01209R1 Antiretroviral treatment failure and associated factors among people living with HIV on therapy in Homa Bay, Kenya: A retrospective study PLOS Global Public Health Dear Dr. Masaba, Thank you for submitting your manuscript to PLOS Global Public Health. After careful consideration, we feel that it has merit but does not fully meet PLOS Global Public Health’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. The reviewer has uploaded a PDF of additional comments that should be addressed. Please review these comments carefully and respond to them in your next submission. Please submit your revised manuscript by Feb 16 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 globalpubhealth@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pgph/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised 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, Sanghyuk S Shin Academic Editor PLOS Global Public Health Journal Requirements: 1. 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. 2. We have noticed that you have uploaded Supporting Information files, but you have not included a list of legends. Please add a full list of legends for your Supporting Information files after the references list. Additional Editor Comments (if provided): [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: All comments have been addressed ********** 2. Does this manuscript meet PLOS Global Public Health’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 ********** 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 (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: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS Global Public Health 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) ********** 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 #1: Yes: Marcel Kitenge ********** Please see the reviewer's comments submitted in PDF format. [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 |
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Antiretroviral treatment failure and associated factors among people living with HIV on therapy in Homa Bay, Kenya: A retrospective study PGPH-D-22-01209R2 Dear Dr Masaba, We are pleased to inform you that your manuscript 'Antiretroviral treatment failure and associated factors among people living with HIV on therapy in Homa Bay, Kenya: A retrospective study' has been provisionally accepted for publication in PLOS Global Public Health. Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests. 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 globalpubhealth@plos.org. Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Global Public Health. Best regards, Sanghyuk S Shin Academic Editor PLOS Global Public Health |
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