Preferences for services in a patient’s first six months on antiretroviral therapy for HIV in South Africa and Zambia (PREFER): research protocol for a prospective observational cohort study

Background For patients on HIV treatment in sub-Saharan Africa, the highest risk for loss from care remains the first six months after antiretroviral (ART) initiation, when patients are not yet eligible for differentiated service delivery (DSD) models that offer lower-burden, patient-centred care and thus improve treatment outcomes. To reduce early disengagement from care, the PREFER study will use a sequential mixed-methods approach to describe the characteristics, needs, concerns, and preferences of patients in South Africa and Zambia 0-6 months after ART initiation or re-initiation. Protocol PREFER is an observational, prospective cohort study of adults on ART for ≤6 months at 12 public healthcare facilities in Zambia and 18 in South Africa. Its objective is to describe and understand the needs and preferences of initiating and re-initiating ART clients to inform the design of DSD models for the early HIV treatment period, improve early treatment outcomes, and distinguish the barriers encountered by naïve patients from those facing re-initiators. It has four components: 1) survey of clients 0-6 months after ART initiation (identify characteristics and preferences of clients starting ART); 2) follow up through routinely collected medical records for <24 months after enrollment (describe resource utilization and patterns and predictors of engagement in care); 3) focus group discussions and discrete choice experiment (explore reported barriers to and facilitators of retention); and 4) in South Africa only, collection of blood samples (assess the prevalence of ARV metabolites indicating prior ART use). Conclusions PREFER aims to understand why the early treatment period is so challenging and how service delivery can be amended to address the obstacles that lead to early disengagement from care. It will generate information about client characteristics and preferences to help respond to patients’ needs and design better strategies for service delivery and improve resource allocation going forward.


Introduction
Rapid, same-day, and community-based initiation of antiretroviral therapy (ART) for HIV has shifted the challenge of achieving optimal outcomes in HIV treatment onto retention in care after a patient has started ART.The highest risk for loss from care consistently remains a patient's first six months after ART initiation 1 .Dubbed the "early retention" period 2 , this interval accounts for roughly three quarters of all first-year attrition from HIV programs in sub-Saharan Africa 3 .In South Africa, 26% of patients were lost to follow up by 6 months after initiation in a recent trial of a case management intervention 4 , and attrition was 35.6% by 6 months in a recent observational study 5 .
Patient characteristics and service delivery characteristics both contribute to high attrition during the early treatment period 1 .After the World Health Organization (WHO) began recommending universal treatment access in 2016, the median CD4 count of new ART initiates rose substantially, reflecting the much higher proportion of asymptomatic, "healthy" patients than in the past 6 , despite a fairly consistent minority of a quarter to a third continuing to present with very low CD4 counts 7,8 .The proportion of patients who are re-initiating ART after previously interrupting care is also climbing.A recent modeling exercise estimated that in 2020, fully 58% of those who tested positive for HIV were already aware of their positive status 9 and thus may have declined an earlier opportunity to start or remain on treatment.Two small studies in South Africa identified ARV metabolites-evidence of recent exposure to ARV medications-in 53% and 19% of self-reported naïve ART initiators in Limpopo and KZN provinces, respectively 10,11 .Individuals who know their HIV-positive status but are not on ART likely face multiple barriers to starting treatment; those who both know their status and have already started and stopped ART at least once (re-initiators) may require additional support to remain in care once they re-initiate care.
The service delivery landscape has transformed at many points in the HIV treatment cascade in recent years, most notably through the introduction of rapid and same-day ART initiation for those not yet on treatment 12 and the development of patientcentred differentiated service delivery (DSD) models for those already established on ART for at least 6 months 13 .Neither same-day initiation nor most current DSD models, however, offer solutions for patients during the first six months after initiation 14 .The model of care for the early treatment period that is offered to most newly-initiating and re-initiating patients has evolved little from its original outlines, though COVID-19 restrictions precipitated some reductions in required numbers of clinic visits and increases in dispensing intervals 15 .
A first step in designing new models of care for the early treatment period is to gain a comprehensive understanding of patients' needs, concerns, resources, and preferences for service delivery during this period.Treatment and retention in the first 6 months after ART initiation could be improved if patients were triaged to receive more or less support based on a combination of known risks to retention in care and patient preferences for how little or how much interaction, and what kinds of interaction, with the health system are desired.
In the PREFER study, we will use a sequential mixedmethods approach to survey a sample of patients in South Africa and Zambia at various points between months 0 and 6 after ART initiation to develop a detailed profile of different groups of patients who may be best served by different models of care.The specific objectives of the study include describing the characteristics and preferences of new and re-initiating ART clients, exploring their concerns in depth through focus groups, identifying associations between client characteristics and early treatment outcomes, and assessing differences between naïve and non-naïve treatment initiators.

Protocol
Overview PREFER is an observational, prospective cohort study in South Africa and Zambia that aims to inform the design of service delivery models for the early HIV treatment period.Its primary objective is to describe and understand the needs of initiating and re-initiating ART clients in order to inform the design of DSD models for the early HIV treatment period and improve early treatment outcomes.It has four components: 1) a survey of clients during the period from 0 to 6 months after ART initiation; 2) follow up through routinely collected medical records for a maximum of 12 or 24 months after study enrollment, depending on the study country; 3) focus group discussions (FGDs) and a discrete choice experiment (DCE) to explore specific issues raised in the survey; and 4) in South Africa only, collection of blood samples from a subsample of who self-report that they are not currently on ART and are initiating ART on the day of study enrollment to assess the prevalence of ARV metabolites indicating prior ART use (Figure 1).
Study sites PREFER will be conducted at 18 healthcare facilities in South Africa and 12 in Zambia (Table 1).Study sites represent the facilities participating in the SENTINEL study of the AMBIT Project 16 .For SENTINEL, local study teams first

Amendments from Version 1
This revised version of the manuscript responds to reviewers' suggestions about clarifying the objectives of the study, providing more information about the consent process and data confidentiality, and adding to the discussion of the study's potential impact.It also describes a newly added sub-component of the study, a discrete choice experiment that was added to the focus group discussions.A flow chart (figure) was added to help clarify study procedures, and two additional supplementary files were provided.identified provinces and districts that were accessible, had a high burden of HIV, utilized the national electronic medical record system, and jointly provided diversity in setting (rural, urban), facility size, and nongovernmental support partners.Within each district, SENTINEL then selected a set of facilities that represented the desired diversity and were large enough to provide the sample sizes required.These were chosen with engagement from the relevant Departments and Ministries of Health, including national and district government health officials with responsibility for the sites.Further information about SENTINEL and preliminary results can be found at www.sites.bu.edu/ambit.

Study population, informed consent, and enrollment
We will sequentially recruit adult (≥18 years old) ART patients on treatment for ≤6 months who present at the study sites for ART initiation, routine care, or unscheduled HIV-related care and provide written informed consent.We will exclude anyone who is unable to communicate in any of the languages into which the survey has been translated, is unwilling to take the time required to complete the survey on the day of consent, or who, in the opinion of study staff, is physically, mentally, or emotionally unable to participate in the study.Eligibility will be determined through completion of a survey screening form, which will also allow us to compare the sex and age distribution of the population enrolled in the survey with those of the full potentially eligible population (Extended data -Supplementary file 1).
At the study sites, clinic staff will inform potentially eligible patients that they may be eligible to participate in a research study when the patient checks in at the reception desk (i.e. as they enter the facility and make their initial contact with facility staff).Patients will be recruited consecutively as they arrive at the facility, based on availability of study interviewers.We expect this process to generate a representative sample of patients over the course of each enrollment day, accurately reflecting the diversity of eligible potential participants.
Written informed consent will be sought from all eligible participants, covering the survey, medical record review, agreement to be contacted for later focus group participation, and agreement to blood sample testing for prior ARV exposure (Extended data -Supplementary file 2).Participants will be informed of the risks or discomforts that may come from study participation, their rights as participants, data security and confidentiality, and information to contact the study team if questions or concerns arise.The consent process and questionnaire will be administered in a confidential space by a trained research assistant in a private location at the clinic during the periods while patients are waiting in queues for facility services (consultations or medication pickups).Participants will be assured that they will not lose their places in the queue as a result of study participation.
Patients who start the survey but do not have time to complete it before reaching the front of the queue will be asked to return to the research assistant after receiving services, in order to complete the survey.We anticipate that each interview will last 75 minutes, including the consent process.Participants will be offered light refreshments during the study and will be given a token valued at approximately US$10 to thank them for their time and participation.

PREFER survey of client characteristics and preferences
The PREFER survey instrument aims to describe the characteristics, experiences, concerns, and preferences of clients initiating or re-initiating ART.It will be a structured questionnaire designed for primarily quantitative analysis but with some open-ended questions (Extended data -Supplementary file 3).Questions will build on previous work of the AMBIT Project and on the authors' experience in studying retention in HIV care 1,3,[17][18][19] .The questionnaire has eight substantive sections, addressing the respondent's demographics and socio-economic status, HIV testing history, HIV treatment history, current HIV care and treatment experience, other healthcare, preferences for features of treatment delivery, expectations, and costs of seeking care.Questions are designed to elicit information about participants' past experiences with the healthcare system and identify changes that would potentially improve their future experiences.
As PREFER is a descriptive study that aims to describe participants' self-reported experiences and preferences, rather than comparing outcomes or testing a hypothesis, sample sizes were chosen to optimize the use of study resources and time availability.Using the expected number of eligible patients at each study site, the number of such patients who are expected to visit the sites during the data collection period, and an anticipated data collection period of 90 days in each country, the study protocols allow a maximum enrollment of 2,500 participants per country.We anticipate that actual enrollment will be somewhat less than this, with a minimum target of an average of 50 participants per study site, or 900 in South Africa and 600 in Zambia; we expect these sample sizes to be sufficient to generate sufficiently precise results to the survey's quantitative questions.

Medical record review for outcomes and resource utilization
Using identifiers collected as part of the structured questionnaire, we will also collect follow up data from routine medical records for the period from each participant's initial data entry (first presentation for testing or care) to 12 months after study enrollment, with an additional round of medical record data collection up to 24 months after study enrollment in South Africa.The objective of this component of the study is to describe early treatment outcomes and, using data from the survey, identify associations between client characteristics and their outcomes, in order to better match early treatment interventions with client needs.
Medical record data will be drawn from Tier.Net in South Africa and Smartcare in Zambia, paper records and registers maintained at the study sites, and other databases, such as South Africa's National Health Laboratory Services database, to ascertain whether patients are retained in care during the first 6 months on ART.We will collect data on HIV treatment history and current engagement, medications dispensed, laboratory tests performed, comorbidities, and other healthcare provided by the site and recorded in the EMR during the study period.We note that the EMRs in both countries are largely limited to HIV care; they may capture data on tuberculosis and other conditions but generally do not contain information about services provided by other departments within the clinics.
Post-enrollment focus group discussions to explore clients' concerns and preferences Participants will be asked during the consent process for their agreement to be contacted by telephone or e-mail at any time during the 12 months following study enrollment and invited to participate in a FGD.Focus groups will address the concerns raised by survey participants to explore in-depth the challenges clients face in the early treatment period.
We anticipate inviting up to 300 participants to participate in FGDs of up to 10 participants in each of up to 30 groups, 15 per country.We will purposively select PREFER sites which have sufficient numbers of enrollees and represent a diversity of settings and purposively identify participants who have a record of missed visits or who have expressed concerns about their care in the quantitative survey.Patients will be contacted by telephone or email, depending on their preference stated at enrollment.Study staff conversant in English and the appropriate local language and trained in qualitative research methods and human subjects protection will conduct the FGDs.
Before commencing the FGD, all participants will be briefly screened for eligibility and study staff will proceed with the informed consent process.We will document informed consent with a signature or a thumb-print and capture basic demographic information for each participant to allow linkage to their survey results.FGD leaders, who will be trained study research assistants, will remind all participants that anything said during the discussion must remain private and should not be shared beyond the group.The FGDs will conducted in a private setting in the clinic or community.
To guide the discussion and probe for more in-depth responses, FGD leaders will use an FGD guide developed based on responses to the PREFER survey and focusing on specific issues or concerns that participants raise in the survey (Extended data -Supplementary file 4).Anticipated topics, which may vary by country, include HIV treatment experience, patient preferences for receiving HIV treatment, and patient expectations of HIV care.The FGD will be audio recorded and the leaders will also take notes during the interview.FGDs should take no longer than two hours.
Prior to starting the focus group discussions, participants will also be asked to participate in a brief discrete choice experiment (DCE) to rank their specific preferences for features of treatment delivery, such as visit frequency and medication refill duration and location, in the first six months of care.The DCE will provide a series of hypothetical scenarios for receiving ART, each of which contains a combination of attributes that emerge as important in the survey, which we expect to include location, waiting time, months of ART dispensed at a time, friendliness of providers, cost, and/or other attributes.The DCE instrument will include a maximum of 10 attributes with no more than three response levels each.Each participant will evaluate a maximum of nine choice sets-two scenarios with a different hypothetical combination of attributes-with one repeated to check for internal consistency (Extended data -Supplementary file 5).Participants will select their preferred option, then be asked if they would use that option if it were available.We expect the DCE to take approximately 15 minutes per participant and to be administered in a quiet, private space before the FGD commences.DCE results will be combined with FGD outcomes to develop a more nuanced description of clients' needs and preferences.
Biological sample collection at South African sites to estimate prior ART exposure For a subsample of South African study participants who are enrolled on the day of ART initiation or re-initiation who self-report as ART-naïve or not having been on treatment for a least 90 days, a dried blood specimen (DBS) will be collected from PREFER survey participants at some study sites.The objective of this component of the study is to add to the evidence base about the proportion and characteristics of the large group of clients who have prior ART experience but do not reveal this to healthcare providers.As these clients have, by definition, previously faced barriers to ART retention, understanding more about them is essential to improving early treatment outcomes.
Sites were chosen based on willingness of providers to create the dried blood spots after obtaining venous blood sample for routine ART initiation blood tests.Blood is drawn routinely as part of the standard of care ART initiation process in South Africa.DBS specimens will be extracted from the routinely collected blood samples drawn by existing clinic staff (nurses or phlebotomists), who are trained in safe and sterile collection techniques.For the study, a sample of 50μml will be extracted from an existing EDTA vacutainer tube with a capillary tube and placed onto a Whatman Protein 903 filter paper.A minimum of 3 dried blood spots will be completed for each patient.Specimens will be allowed to air dry for 2 hours after being taken, or according to assay instructions.Specimens will be covered with glycine weighing paper after drying.Collected, dried specimens will be stored in a -4°C freezer and be shipped in 6-weekly batches via courier to the University of Cape Town Division of Pharmacology, PK Laboratory for analysis.Specimens will be batch-screened for the presence of tenofovir diphosphate.
Participants who meet the inclusion criteria for this subsample (initiating or re-initiating ART and self-reporting as ART-naïve or not having been on treatment for HIV for at least 90 days) will be consecutively enrolled up to a maximum of 200 participants from all participating study sites combined.Enrollment in this subsample will begin when the consumables required for DBS creation have been procured and staff have been trained on standard operating procedures for creating a DBS.Consent for biological sample collection is included in the overall survey consent form.

Data management
A screening register will be kept by the study research assistants to record the consent process and keep track of those who do not consent, to allow us to determine if our sample is biased by patient characteristics due to differential consent.The screening register will not contain any individual identifiers.It will request age category, gender, and months on ART, as needed to determine survey eligibility only.
Patient survey responses will be entered live at the time of the interview into an electronic database on Survey CTO (Dobility 2023) using handheld tablets.If there are power failures, data will be entered onto paper study forms and then transcribed into a database at the local study office.Survey data will be converted to SAS, STATA, or R for final cleaning and data analysis.All analytic databases will be password protected with access restricted to the members of the study team.All survey respondents will be assigned a seven-digit, sequential identification number.The study ID number will be used to identify individual subjects in the study databases and to link survey response data to patient retention outcomes data and for all data analysis.Once data are linked, identifiers will be removed from the analysis file and all subjects will be assigned a random study ID, which will be used for all analysis.
FGD audio files will be transcribed verbatim, then transcribed and translated into English for analysis.
Data for this study will be accessible only by key study personnel.Study ID numbers will be used in place of names or identifying information to safeguard participants' privacy.All physical consent forms, questionnaires, and notes will be stored in locked cabinets, with access restricted to study personnel.All data will be collected on encrypted devices and stored on secure drives, with access restricted to study personnel.A fully anonymized data set may be posted to a public data repository when the protocol has been closed, if required by the funder and journal.

Data analysis and dissemination
We will first create a descriptive summary of the demographic and clinical characteristics of participants enrolled in the study and responses to each question using frequencies and simple proportions for categorical variables and medians with interquartile ranges for continuous variables.We will then stratify these baseline survey responses by site characteristics, time on ART, self-reported naïve v non-naïve treatment status, and/or patient characteristics such as age and sex, as data allow.Data will not be pooled across countries, but differences in results by country will be noted and discussed.
Utilizing follow up data collected from patient medical records, we will conduct a crude analysis reporting simple proportions with 95% confidence intervals of patients disengaging from care, defined as missing a scheduled clinical or medication pickup visit during the first 6 months after treatment initiation by more than 28 days.Next, we will compare the proportions of patient disengaged from care by key variables including age, gender, clinical stage at ART initiation, site characteristics, time on ART, and naïve v non-naïve treatment status.
If enrollment numbers allow, the analysis will include a simple unadjusted comparison of outcome groups (retained or disengaged) with respect to baseline predictors of outcomes.Potential predictors include demographic and clinical variables and geographic and facility-level factors (urban vs rural setting, facility type).Using a log-linear regression model, we will next estimate crude risk ratios and crude risk differences and their corresponding 95% confidence intervals.If any important differences are observed, we will proceed with an adjusted model.Should crude stratification techniques reveal potential effect measure modification, these analyses will not be adjusted but rather reported as stratified output.
For the FGD output, we will conduct a content analysis of the qualitative data using the Framework Method 20 .We will use a combination inductive-deductive approach wherein most codes will be identified a priori, aligned with the FGD guide and literature, but the coding process will allow for additional codes to emerge to form a final analytical framework.Data will be charted, summarized, and quotations will be presented to illustrate key points when appropriate.Results will be presented stratified by country and urbanicity of sites.
To analyze the DCE survey data collected before the FGDs, we will estimate the impact of each attribute on a participant's choice using a conditional logit model and a random effects probit model.The DCE results will be triangulated with the survey and FGD finding to complement PREFER overall conclusions about client preferences.
For the analysis of prior ART exposure, the presence of TDF above 0.02µg/ml in blood samples will be considered as positive for previous ART use in the previous 3 months or as advised by the laboratory.We will report the proportion of those who have evidence of usage of TDF and, where possible, use the quantified measure to estimate frequency of ART usage, in the preceding 90 days.If sample size allows, we will also identify client characteristics associated with prior ART exposure, using survey responses and medical records.
The study results will be disseminated in several ways.The primary audiences for the results of this study are the South African National Department of Health and Zambian Ministry of Health and their partners, who will use the findings to improve retention in care during the early treatment period.In addition, we will use the results to inform the design of one or more new models of service delivery, which we expect to implement and evaluate during a later stage of this project.Many of the findings will also likely be of broader interest in South Africa and other countries and will be made as widely available as possible, through journals, websites, and conferences.Only aggregated, stratified data will be presented; it will not be possible to identify any individual patients from any of the results that are presented.

Limitations
We anticipate that the PREFER study will have a number of limitations.First, the target sample size is small, in terms of both number of study sites and number of participants, and generalizability to districts and provinces not included in the survey will require caution.Second, survey participants will provide responses about their experiences up to 6 months after ART initiation, creating the possibility of recall bias for questions pertaining to HIV testing and other pre-ART events.Third, we will largely rely on participant self-report to determine prior ART use.Several studies have demonstrated underreporting of prior ART use by self-report which could result in exposure misclassification for analyses stratified by prior treatment status.While we plan to do dried blood sampling to measure ART metabolites for prior ART exposure, the subsample who will be tested will be too small to stratify by patient or facility characteristics.Fourth, as we can only enroll participants actively participating in ART care at health facilities, the study will not capture the experiences and perceptions of individuals who have already disengaged from care.While we will be able to observe re-initiators, those who have not returned to the initiating facility will not be enrolled, potentially limiting our understanding of those who have disengaged from care.Fifth, we will utilize routinely collected EMR data to ascertain participant ART retention outcomes at 6 months after ART initiation.While efficient in terms of resources, this approach is limited to data observed at the initiating facility and will not observe participants accessing care at other facilities.Silent transfers such as these may result in outcome misclassification among some classified as disengaged.

Ethics review
The

Conclusions/discussion
Many sub-Saharan African countries have achieved the first and third of the "three 90s" 21 -HIV testing and viral suppression among those remaining on treatment--that represented global targets for HIV programs during most of the decade of the 2010s.The second of the 90s-initiating and maintaining at least 90% of known HIV-positive people on ART-has remained out of reach for countries like South Africa and Zambia, in part due to high rates of disengagement from care after treatment initiation.For some countries, improving retention in care may be the only effective option for achieving current targets 22 , which have been revised to the "three 95s" 23 .To do this, attrition from care during the early treatment period-patients' first six months on ART-must be reduced.
The PREFER study aims to understand what is happening during the early treatment period on the ground, as individual healthcare facilities interpret and implement national guidelines and healthcare workers and clients adapt to new medication regimens and new models of service delivery.PREFER was designed to understand why the early treatment period is so challenging for many patients and how service delivery can be amended to address the obstacles that lead to early disengagement from care, be they out-of-pocket costs, fear of disclosure, poor provider relations, or other concerns, and to distinguish the barriers encountered by naïve patients to those facing re-initiators.
Once the analysis has been completed, we expect to disseminate the findings from this research as broadly as possible in countries facing similar challenges with early treatment outcomes as those faced by South Africa and Zambia.Findings will be reported at project transition workshops held for local stakeholders in each country, including recipients of care, Ministries of Health, implementing partners and research organisations.Policy briefs will also be available on the project website.Within Retain6, we expect to use the information collected by PREFER to inform the second phase of the project, during which we will evaluate interventions to improve early treatment outcomes.The information collected by PREFER will also help policy makers and program managers respond to patients' needs and design better strategies for service delivery and improve resource allocation going forward.
Introduction: The introduction is extremely well written and logical.The study appears highly relevant and well justified.The study design seems appropriate.However, as previously suggested, I think the introduction could benefit by ending with a list of specific objectives (beyond the general overarching goals mentioned), that would better contextualize and prepare the reader for the data collection and planned analyses sections.There are hints of these interspersed throughout the text and their consolidation in one location would be helpful.Indeed, the different data collection methods and analyses could be headed by their respective objective, as a guide.
Protocol: Some questions about study methodology could be addressed, for instance, is patient compensation for study participation provided?More could also be said about the origins and construction of the PREFER survey.How was the content developed or chosen -who was involved?
Were instruments with evidence of validity used?Were patients involved in piloting or choosing the survey content?
Is the rationale for, and objectives of, the study clearly described?Yes Is the study design appropriate for the research question?Yes

Are sufficient details of the methods provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?

Not applicable
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: HIV, patient-reported outcome measures, qualitative methods, antiretroviral therapy adherence and its barriers, stakeholder engagement, implementation research I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

Introduction:
The manuscript effectively highlights the importance of the research question by describing the challenges of patient retention during the early phase of ART.It also emphasizes the significance of understanding patient preferences during this period. 2.

Methods:
The manuscript provides a comprehensive overview of the study methods.However, it would be beneficial to clarify the sampling strategy in more detail, including how sites and participants were selected.Additionally, it might be useful to include a flowchart or diagram to illustrate the study design and data collection process. 3.

Data Collection:
The methods section mentions that a dried blood specimen will be collected from a subsample of South African participants.It would be helpful to specify how this subsample will be selected and how the blood samples will be used in the analysis.

Potential Improvements
The research protocol could employ Focus Group Discussions (FGDs) to understand the reasons behind loss from care in the first six months after antiretroviral (ART) initiation, this comes along with quite a number of limitations of FGDS; Proposed research questions.
a) Why is the early treatment period (first six months of ART initiation) challenging?b) How can service delivery be amended to address the obstacles that lead to early disengagement from care? c) What are the patient's preferences for healthcare services during the initial six months of 4.
ART treatment.? d) What are the barriers encountered by naïve patients to those facing re-initiators?The information collected by PREFER will help respond to patients' needs design better strategies for service delivery and improve resource allocation going forward.
Ethical Considerations: While the manuscript mentions that the study was approved by relevant ethics committees, it would be beneficial to provide more information about the informed consent process, including how participants were informed about the study and their rights as participants. 5.

Data Management:
The manuscript briefly discusses data management but does not mention data security and privacy.It would be important to highlight the steps taken to protect the confidentiality and privacy of participants' data. 6.

Data Analysis:
The manuscript outlines the planned data analysis, including both quantitative and qualitative components.However, it would be helpful to mention specific statistical methods that will be used for data analysis.

Conclusion:
The conclusion section effectively summarizes the study's objectives and potential impact on improving retention in HIV care.The manuscript could elaborate on the broader implications of the study's findings for HIV programs in sub-Saharan Africa. 8.

Tables and Figures:
It would be beneficial to include tables or figures to visually represent key information, such as the study sites, participant demographics, or the data collection process.

9.
References: Unable to comment on the references as the journal review guidelines do not mention the type of referencing required.

10.
Overall, the manuscript provides a well-structured and informative research protocol.Addressing the above points will enhance the clarity and completeness of the manuscript.
Is the rationale for, and objectives of, the study clearly described?Yes

Are sufficient details of the methods provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Infectious diseases, Epidemiology, clinical trials, global health, refugee health, for which the PREFER sites were originally chosen, has been published and explains the selection process in a bit more detail.We now cite that paper to provide further information for readers.
Selection of participants is described on page 6.We have tried to clarify the steps and added additional information about the consent process.We thank the Reviewer for the suggestion of a flowchart, which we have now added to the Methods section as Figure 1.

Data Collection:
The methods section mentions that a dried blood specimen will be collected from a subsample of South African participants.It would be helpful to specify how this subsample will be selected and how the blood samples will be used in the analysis.
Response: We apologize that the previous version did not clearly state how we would select the subsample.We identified 3 sites (one in each province) within our 18 participating facilities that had providers who were willing to attend training and create DBS using the venous samples they collected as part of the routine blood test performed at ART initiation.Clients enrolling at these facilities who meet the inclusion criteria for PREFER and enroll on their day of ART initiation after the necessary supplies to create DBS specimens are procured and facility staff have been trained will be enrolled consecutively.We have added language to clarify this (page 8) and to describe how we will use the data to estimate the proportion who have evidence of recent ART usage (page 9).Response: Thank you for this suggestion.The research protocol does employ FGDs, as described on page 7.Your suggested research questions are similar to those in our FGD guide, which we have now added as a supplemental file.In addition, after submitting the original version of this manuscript for review, we decided to include a brief discrete choice experiment for focus group participants.This is now described in detail in the same section of the manuscript.

Ethical Considerations:
While the manuscript mentions that the study was approved by relevant ethics committees, it would be beneficial to provide more information about the informed consent process, including how participants were informed about the study and their rights as participants.

Response:
The informed consent process is described on page 6.To provide the additional information requested, we have now added the following sentences: "Participants will also be informed of the risks or discomforts that may come from study participation, their rights as participants, data security and confidentiality, and information to contact the study team if questions or concerns arise.""Participants will be offered light refreshments during the study and will be given a token valued at approximately US$10 to thank them for their time and participation."

Data Management:
The manuscript briefly discusses data management but does not mention data security and privacy.It would be important to highlight the steps taken to protect the confidentiality and privacy of participants' data.
Response: Thank you for this suggestion.We have added the following paragraph to the data management section (page 9): "Data for this study will be accessible only by key study personnel.Study ID numbers will be used in place of names or identifying information to safeguard participants' privacy.All physical consent forms, questionnaires, and notes will be stored in locked cabinets, with access restricted to study personnel.All data will be collected on encrypted devices and stored on secure drives, with access restricted to study personnel.A fully anonymized data set may be posted to a public data repository when the protocol has been closed, if required by the funder and journal." 6. Data Analysis: The manuscript outlines the planned data analysis, including both quantitative and qualitative components.However, it would be helpful to mention specific statistical methods that will be used for data analysis.
Response: Page 9 of the manuscript lays out the analysis plan, including proposed general methods.More specific statistical methods will depend to some extent on the data, and in particular our success in linking survey data and medical records for each participant.As is described in the manuscript, we expect to perform crude and adjusted log-linear regressions.Other methods may be used as deemed relevant by the study team once data have been cleaned and descriptive statistics generated.

Conclusion:
The conclusion section effectively summarizes the study's objectives and potential impact on improving retention in HIV care.The manuscript could elaborate on the broader implications of the study's findings for HIV programs in sub-Saharan Africa.
Response: Thank you for this suggestion.We did describe our plan to disseminate findings from this work (page 10).It is difficult to discuss the implications of the research before we know the results.To better explain the potential implications, though, we have outlined how we plan to engage local stakeholders with our findings prior to moving to phase 2 of the Retain6 project, as follows: "Once the analysis has been completed, we expect to disseminate the findings from this research as broadly as possible in countries facing similar challenges with early treatment outcomes as those faced by South Africa and Zambia.Findings will be reported at project transition workshops held for local stakeholders in each country, including recipients of care, Ministries of Health, implementing partners and research organizations.Policy briefs will also be available on the Retain6 website.Within Retain6, we expect to use the information collected by PREFER to inform the second phase of the project, during which we will evaluate interventions to improve early treatment outcomes.The information collected by PREFER will also help policy makers and program managers respond to patients' needs and design better strategies for service delivery and improve resource allocation going forward."

Tables and Figures:
It would be beneficial to include tables or figures to visually represent key information, such as the study sites, participant demographics, or the data collection process.
Response: Thank you.Table 1 describes the study sites.We do not yet have information about participant demographics, as this is a protocol for prospective enrollment.We have added a figure to visually represent the data collection process (Figure 1) and hope that this will improve the clarity of our manuscript.

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References: Unable to comment on the references as the journal review guidelines do not mention the type of referencing required.

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Potential Improvements.The research protocol could employ Focus Group Discussions (FGDs) to understand the reasons behind loss from care in the first six months after antiretroviral (ART) initiation, this comes along with quite a number of limitations of FGDS;Proposed research questions.a) Why is the early treatment period (first six months of ART initiation) challenging?b) How can service delivery be amended to address the obstacles that lead to early disengagement from care? c) What are the patient's preferences for healthcare services during the initial six months of ART treatment.? d) What are the barriers encountered by naïve patients to those facing re-initiators?The information collected by PREFER will help respond to patients' needs design better strategies for service delivery and improve resource allocation going forward.

. PREFER study sites. Facility Setting ART patients as of August, 2021 Average ART initiates per month, 2021 South Africa
Figure 1.Components and flow of the PREFER study.
PREFER study was approved with a separate protocol for each study country by the Boston University Institutional Review Board (South Africa H-42726, May 20, 2022; Zambia H-42903, July 11, 2022) and by the University of the Current status of the study Enrollment in the PREFER survey began on September 7, 2022 in South Africa and September 21, 2022 in Zambia.We anticipate that the quantitative survey will be completed in May 2023 and all data collection by August 2023.At the time of submission of the first version of the manuscript, data collection for the quantitative survey is ongoing; data collection for the medical record review, focus group discussions, and biological samples has not yet started.