Resistance Testing Versus Adherence Support for Management of Patients With Virologic Failure on First-Line Antiretroviral Therapy in Sub-Saharan Africa
Phase: NA
Conditions: HIV, AIDS
Sponsor: Massachusetts General Hospital

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RESEARCH PROTOCOL 
 
 
REVAMP: 
Resistance Testing Versus Adherence Support for Management of Patients with 
Virologic Failure on First-Line Antiretroviral Therapy in sub-Saharan Africa 
 
An open-label randomized controlled trial 
 
 
 
 
 
Harvard Medical School 
Massachusetts General Hospital 
Mbarara University of Science and Technology 
University of KwaZulu-Natal 
Emory University 
University of Rochester 
Africa Health Research Institute 
University of California San Francisco 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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TABLE OF CONTENTS 
 
 
 
I. Investigators  and Institutions ………………………………………………………………………..……….…….4 
 
II. Project Summary and Specific Aims……………………………………………………………………...……….6 
 
III. Background and Significance…………………………………………………………………………………..……7 
 
IV. Study Design and Subject Selection……………………………………………………………………………….9 
 
V. Study Procedures for Patients Randomized to Standard of Care Arm……………………..……13 
 
VI. Study Procedures for Patients Randomized to Resistance Testing Arm……………………...15 
 
VII. Data Collection and Management……………………………………………………….………….……..…….18 
 
VIII. Study Monitoring and Quality Assurance……………………………………………………………..……23 
 
IX. Statistical Considerations and Analysis……………………………………………………………………..…24 
 
X. Human Subjects Considerations………………………………………………...………………..…….…...……..27 
 
XI.  References………………………………………………………………………….……………………….....…..……….29

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ABBREVIATIONS 
 
 
 
 
ART 
Antiretroviral therapy 
 
 
DALY 
Disability adjusted life year 
 
 
DBS 
Dried blood spot 
 
 
EDTA 
Ethylenediaminetetraacetic acid 
 
 
 
Β-HCG 
β-human chorionic gonadotropin 
 
 
II 
Integrase inhibitor 
 
 
ISPOR 
International Society of Pharmacoeconomics Outcomes Research 
 
 
ISS 
Immune suppression syndrome 
 
 
 
JCRC 
Joint Clinical Research Centre 
 
 
 
ml 
Milliliter 
 
 
MRRH 
Mbarara Regional Referral Hospital 
 
 
NHLS 
National Health Laboratory Services 
 
 
 
NNRTI 
Non-nucleoside reverse transcriptase inhibitor 
 
 
PEPFAR 
President’s Emergency Plan for AIDS Relief 
 
 
PI 
Protease inhibitor 
 
 
SOC 
Standard of care 
 
 
RT 
Resistance testing 
 
 
UKZN 
University of KwaZulu-Natal 
 
 
UNAIDS 
Joint United Nations Programme on HIV/AIDS 
 
 
VF 
Virologic failure 
 
 
WHO 
World Health Organization 
 
 
 

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I. INVESTIGATORS AND INSTITUTIONS 
 
A. Massachusetts General Hospital / Harvard Medical School 
 
 
Mark J. Siedner, MD MPH: Co-Principal Investigator 
 
 
Tel: +1-617-726-4686; 
Email: msiedner@mgh.harvard.edu 
Rajesh Gandhi, MD: Co-Investigator, Protocol HIV Clinician 
 
 
 
 
 
Email: rgandhi@mgh.harvard.edu 
Kevin Ard, MD MPH: Co-Investigator, Protocol HIV Clinician 
 
 
 
 
 
 
 Email: kard@partners.org 
 
Suzanne McCluskey, MD: Co-Investigator 
 
 
 
 
 
 
Email: smccluskey@mgh.harvard.edu 
 
Jonathan Li, MD PhD: Co-Investigator, Sub-Study Virologist 
 
 
 
 
 
 
Email: jli@bwh.harvard.edu 
 
Bethany Hedt-Gauthier: Co-Investigator, Sub-Study Biostatistician 
 
 
 
 
 
 
Email: Bethany_Gauthier@hms.harvard.edu 
 
 
B. Mbarara University of Science and Technology 
 
 
Winnie Muyindike, MBChB MMed: Co-Principal Investigator 
 
 
Tel: +256-772-521-619; 
Email: wmuyindike@gmail.com 
 
 
Mwebesa Bosco Bwana, MBChB MPH: Co-Investigator (posthumous) 
 
C. University of KwaZulu-Natal 
 
 
Yunus Moosa, MBChb, PhD: Site Principal Investigator 
 
Tel: +27-31-260-4368; 
Email: moosay@ukzn.ac.za 
 
Pravikrishnen Moodley, MBChB: Co-Investigator, Protocol Clinical Virologist 
Email: moodleyp36@ukzn.ac.za 
Jaysingh Brijkumar, MBBS: Co-Investigator, Protocol South African HIV Clinician 
 
 
 
 
 
Email: jaysingh.brijkumar@kznhealth.gov.za 
Gavin George, PhD: Co-Investigator, Protocol Economist 
Email:  georgeg@ukzn.ac.za 
 
D. Emory University 
 
 
Vincent Marconi, MD: Co-Investigator, Protocol HIV Clinician and Epidemiologist 
Email: vcmarco@emory.edu 
 
E. University of Rochester 
 
 
Brent Johnson, PhD: Co-Investigator, Protocol Statistician 
 
 
 
 
 
Email: brent_johnson@urmc.rochester.edu 
 
F. Griffith University  
 
 
 
Tamlyn Rautenberg, PhD: Co-Investigator, Health Economics 

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Email: t.rautenberg@griffith.edu.au 
 
G. Africa Health Research Institute 
 
 
John Adamson, PhD: Co-Investigator, Therapeutic Drug Monitoring 
 
 
 
 
 
 
Email: john.adamson@ahri.org 
 
H. University of California San Francisco 
 
 
Monica Gandhi, MD MPH: Co-Investigator, Therapeutic Drug Monitoring 
 
 
 
 
 
 
Email: Monica.Gandhi@ucsf.edu 
 
 
 
 

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II. PROJECT SUMMARY AND SPECIFIC AIMS 
 
In an effort to optimize the global HIV care continuum and foster sustained control of the HIV epidemic, 
the Joint United Nations Programme on HIV/AIDS (UNAIDS) has set a “90-90-90” treatment target for 
2020. Achievement of this goal would mean, in part, that 90% of those receiving antiretroviral therapy 
(ART) sustain an undetectable HIV viral load. In sub-Saharan Africa, however, rates of sustained virologic 
suppression remain well below that goal, with 1 in 3 developing virologic failure during the first two 
years of therapy. Patients with virologic failure have higher rates of poor clinical outcomes, increased 
diagnostic and therapeutic costs, and could potentially thwart treatment as prevention strategies. 
Management of virologic failure must be optimized to attain the goal of maintaining 90% on the 
continuum of care. Current WHO guidelines recommend use of viral load testing alone to guide 
management. This strategy possibly promotes unnecessary switching of patients with wild-type virus to 
second-line therapy, while continuing other patients on first-line therapy despite the presence of 
unidentified drug resistance. Yet, whether addition of resistance testing to routine management of 
virologic failure improves outcomes or is cost-effective is unknown. As such, a data-driven approach to 
management of virologic failure, incorporating both efficacy and cost, is needed to address this critical 
gap in knowledge. 
 
The goal of this study is to determine whether addition of routine resistance testing, to guide 
management of virologic failure and sustain the successful completion of the HIV continuum of care, 
improves clinical outcomes and reduces costs for patients with virologic failure on first-line therapy in 
sub-Saharan Africa. We will enroll patients in care at public HIV clinics in Uganda and South Africa who 
have virologic failure on a first-line ART regimen, into a randomized controlled trial to complete the 
following aims: 
 
1) Aim 1: Estimate the effectiveness of resistance test-based management of virologic failure 
(resistance testing arm), versus viral-load based management per WHO guidelines 
(standard of care arm). We hypothesize that resistance testing-based management will be 
superior to standard of care management as measured by the proportion of patients with 
undetectable viral load 9 months after detection of virologic failure. 
 
2) Aim 2: Evaluate the cost effectiveness of resistance-test versus viral load-based 
management of virologic failure in sub-Saharan Africa. We hypothesize that resistance testing 
will be cost effective, because the cost of the assay will be offset by downstream cost savings 
through reduced use of second line therapy. 
 
We intend that results of this study will be a useful resource for public health programmers, ministries of 
health and multinational partners to optimize the clinical management of virologic failure in the region. 
 
 

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III. BACKGROUND AND SIGNIFICANCE 
 
In an effort to optimize the global HIV care continuum and foster sustained control of the HIV epidemic, 
the Joint United Nations Programme on HIV/AIDS (UNAIDS) has set a “90-90-90” treatment target for 
2020 [2]. Achievement of this goal would mean, in part, that 90% of those receiving antiretroviral therapy 
(ART) sustain an undetectable HIV RNA viral load (viral load). At the epicenter of the epidemic in sub-
Saharan Africa, however, rates of virologic suppression remain well below that goal; indeed, a systematic 
review of virologic suppression in the sub-Saharan African region found that only 2 in 3 patients 
maintain virologic suppression over two years of observation [3]. To maintain the goal of achieving 90% 
sustained virologic suppression, management of virologic failure must be optimized. 
 
Yet, the optimal strategy for management of virologic failure in sub-Saharan Africa, in terms of both 
efficacy and cost, is unknown. The 2013 World Health Organization (WHO) HIV treatment guidelines 
recommend monitoring patients in resource-limited settings with viral load measurements at 6 months 
after ART initiation and annually thereafter [1]. Virologic failure is defined as two consecutive viral load 
measurements greater than 1,000 copies/mL, three-six months apart, with adherence reinforcement in 
the interim (Figure 1). The WHO guidelines stipulate that patients meeting this definition of virologic 
failure should switch to second-line ART. These recommendations are likely to have important 
ramifications on management of virologic failure in sub-Saharan Africa as viral load testing becomes 
more widespread through cost reductions [4]. Yet, while viral load testing represents an important 
advance for HIV care in the region [5], it also raises critical questions about the optimal management of 
patients who meet the WHO definition of treatment failure. In particular, the use of viral load 
measurements alone to define treatment failure 
may result in unnecessary switches to costlier 
second-line therapy, potentially imperiling the 
financial sustainability of HIV treatment 
programs. 
 
Rigorous data are lacking to support key aspects 
of WHO guidelines. While some studies have 
found high rates of resistance among those with 
a viral load >1,000 copies/mL on first-line 
therapy [6, 7], others have demonstrated high 
rates of re-suppression without regimen 
switches [2, 8, 9]. Although the recommendation to 
conduct adherence counseling and repeat viral 
load testing prior to switching therapy is meant 
to increase the specificity for detection of 
resistance, this strategy is also unproven. For 
example, a recent study in Swaziland 
demonstrated no additional benefit to 
adherence counseling on re-suppression of 
viremia for those with treatment failure [10]. 
Finally, the requirement for two consecutive 
viral load tests, and the additional clinical 
encounters required to report results and 
conduct clinical decision making, may pose 
Figure 1. World Health Organization schema for 
monitoring and management of treatment failure [1] 

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substantial financial and logistical challenges for patients [11-14].  
Consequently, the current guidelines may introduce substantial delays between detection of virologic 
failure and regimen change, place vulnerable patients at risk for loss to follow-up, and conceivably 
increase the risk of HIV transmission and transmitted drug resistance. An alternate strategy would be to 
perform drug resistance testing as soon as possible after the initial detectable viral load to more precisely 
and promptly guide ART treatment decisions. A group of clinical trials conducted soon after ART became 
standard of care in the United States found that resistance testing improves virologic control and/or CD4 
count response [15-18]. Notably, these studies were conducted solely in resource-rich settings and did not 
consider costs in their assessments. Similar data for the sub-Saharan Africa region are unavailable. 
 
Without resistance testing available, the current guidelines have the potential to result in switching most 
patients with virologic failure to second-line therapy and could confer both patient- and population-level 
risks. For example, most of the region lacks a third-line option for patients who are unable to tolerate PI-
based regimens or are affected by drug-drug interactions with rifampin or other medications. 
Additionally, patients on PI-based regimens require additional clinical monitoring due to the heightened 
risk of metabolic complications [19]. Most important, the financial sustainability of switching large 
populations of patients to second-line therapy is uncertain. If one in three patients initiating ART 
continues to suffer virologic failure within two years [3], treatment programs in the region would be 
charged with supplying second line regimens to over 5 million individuals. 
 
As the President’s Emergency Plan for AIDS Relief (PEPFAR) embarks on its third phase of 
implementation with a focus on sustainability, it is critical to develop a data-driven approach to 
management of virologic failure in sub-Saharan Africa. Although prices for ART have decreased with the 
availability of generic, fixed-dose combination regimens, PI-based second line therapy remains 
approximately 2-3 times as costly as first-line regimens in resource-limited settings (mean regimen costs 
$816 versus $305/year [20]). One report estimated that switching to second-line therapy in Africa was 
unnecessary in approximately one third of cases (i.e., done in the presence of wild-type virus) [21]. While 
preventing these unnecessary regimen switches by routine resistance testing could save funds, this 
strategy would need to be weighed against the cost of resistance testing. 
 
Studies assessing cost-effectiveness of resistance testing in resource-limited settings have demonstrated 
contrasting results, partially due to differing assumptions about its efficacy (Table 1) For example, one 
study demonstrated that the addition of resistance testing was highly cost-effective when wild-type virus 
at failure was relatively common (>12%), and in fact became cost saving when the resistance testing was 
less than $100 per test [22]. A second study demonstrated a cost-neutral effect for the addition of 
resistance testing, assuming a cost of $242 per test, but with resulting clinical benefit to patients [23]. In 
contrast, a third study found no additional benefit to resistance testing over viral load testing alone, even 
with resistance testing costs as little as $30 per test [24]. The variation in results supports the need for a 
well-designed clinical trial with primary data to enable modeling of the economic impact of resistance 
testing in sub-Saharan Africa. 
 
In summary, the increased availability of viral load testing will likely result in sizeable increases in 
identification of virologic failure in sub-Saharan Africa. Without resistance testing, many patients with 
treatment failure, the optimal management of virologic failure remains unknown. The current guidelines 
raise the possibility of frequent switching of patients to second-line therapy with unclear – and 
potentially deleterious – consequences for patients and health systems. 
 

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As PEPFAR shifts its focus to sustainable control of the HIV epidemic, it is crucial to determine the 
efficacy and costs of the current standard of care compared to a resistance-based testing approach for 
management of treatment failure. We designed the current study with the goal of identifying the optimal 
clinical management and allocation of resources for patients with virologic failure to help guide 
ministries of health and multinational partners in the region. 
 
Table 1: Economic Studies Evaluating Resistance Testing in sub-Saharan Africa 
Analysis Model 
Population Perspective 
Time 
Horizon 
Outcome 
Sensitivity 
Analysis 
Primary 
Result 
Cost-Effectiveness 
of Preventing AIDS 
Complications 
state-transition 
model [22] 
South Africa Modified 
societal 
Lifetime 
Cost/year 
of life 
saved 
Univariate and 
multiway 
Very cost 
effective  
Cost minimization 
model [23] 
South Africa Presumed 
Payer 
5 years 
Cost per 
strategy  
Deterministic/ 
Probabilistic  
Cost Neutral 
HIV synthesis 
transmission 
individual-based 
stochastic model 
[24] 
Zimbabwe 
Unstated 
10 years 
Cost/ 
disability 
adjusted 
life year 
(DALY) 
averted 
Several one way 
sensitivity 
analyses 
Not cost-
effective 
 
IV. STUDY DESIGN AND SUBJECT SELECTION 
 
A. Overview 
 
The study design is an open-label, randomized controlled trial. The study will be conducted at study sites 
in Uganda and South Africa. The study population will include HIV-infected patients on first-line 
antiretroviral therapy with a recent viral load >1,000 copies/milliliter (mL). Eligible participants will be 
randomized to the WHO-based standard of care for management of virologic failure or immediate 
resistance testing with use of results to guide ART regimen decisions. The study will add the use of a 
diagnostic test, HIV-1 RNA resistance testing to clinical management of participants in the resistance 
testing arm, but all other clinical care including provision of ART therapy will be done by clinic sites in 
keeping with local HIV guidelines. The primary outcome of interest will be viral suppression (<200 
copies/mL) at 9 months after study enrollment, and will be assessed using an intention to treat analysis, 
where missing or absent results will be considered failures. Secondary outcomes of interest will be viral 
suppression below the limit of assay detection, viral suppression on continuation of first-line (non-
nucleoside reverse transcriptase inhibitor [NNRTI]-based) therapy, drug resistance at study conclusion, 
and mortality, among others. We will analyze primary data collected during the trial to conduct an 
economic analysis with the goal of estimating the cost-effectiveness of resistance testing versus standard 
or care. 
 
B. Study Sites 

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1. Uganda 
 
The Immune Suppression Syndrome (ISS) clinic at the Mbarara Regional Referral Hospital (MRRH) 
and its partner clinic across the street, the Mbarara Municipal Clinic, are PEPFAR-supported clinics, 
which, in combination, follow more than 20,000 patients with HIV/AIDS and have an established clinical 
research infrastructure. The clinics employee over 50 clinical care staff including nurses, clinicians, 
pharmacists, counselors, phlebotomists, patient trackers, and administrative staff. The clinics serve as the 
primary research sites for the MGH-MUST Global Health Collaborative, which employs an additional 60 
research staff with expertise in recruitment, enrollment, participant monitoring, informed consent, data 
collection, phlebotomy, and laboratory storage and testing. 
 
2. South Africa 
 
In Durban, participants will be recruited from the Addington Hospital Sinathando HIV Clinic, 
Clairwood Hospital HIV Clinic, Wentworth Clinic, and King Dinizulu Hospital. The four clinics 
together manage an active caseload of over 10,000 HIV patients. The study will be managed centrally 
from the University of KwaZulu-Natal (UKZN), which operates numerous HIV clinical research projects 
and employs research staff with experience in recruitment, enrollment, participant monitoring, informed 
consent, data collection, phlebotomy, and laboratory processing, storage, and testing. 
 
C. Eligibility Criteria 
 
We will recruit persons with HIV-infection who are in care at any of the five above clinics who meet the 
following inclusion criteria: 
 
1. Inclusion criteria: 
 
a. In care at a public HIV clinic within a PEPFAR-focus sub-Saharan African country (South Africa 
or Uganda) and living within 100 kilometers of the clinic 
b. Age ≥ 18 years at the time of enrollment  
c. Currently prescribed first-line (non-nucleoside reverse transcriptase inhibitor [NNRTI]-based) 
ART for at least 5 months. Switches within first line regimens, including NNRTI and 
nucleos(t)ide backbone changes are allowed. 
d. Detectable plasma viral load > 1,000 copies/mL and/or dried blood spot viral load > 1,000 
copies/mL within 90 days of enrollment 
 
2. Exclusion criteria: 
 
a. Known prior drug resistance 
b. Prior exposure to PI-based ART 
c. Current clinical indication to start PI-based ART 
d. Not planning to remain in the clinic catchment area for the next nine months 
 
3. Eligibility criteria rationale 
 
The study aims to enroll HIV-infected adults on first-line ART with a newly identified instance of a viral 
load >1,000 copies/mL. Patients attending study clinics implementing dried blood spots (DBS) for 

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virologic testing will be eligible, provided they have a DBS viral load >1,000 copies/mL [25, 26], or if they 
undergo repeat plasma viral load testing to confirm a viral load >1,000 copies/mL. We aim to exclude 
those with known prior resistance, those on second line therapy, and those at high risk for default from 
study because of immigration out of the clinic catchment area. 
 
D. Recruitment and Enrollment 
 
We will conduct both passive and active enrollment. For active enrollment, study staff will work in 
partnership with clinic staff to identify potential participants through review of clinic viral load result 
registers for detectable viral loads. In accordance with guidelines in both Uganda and South Africa, 
patients with detectable viral loads will be contacted to return to clinic for immediate care. Potential 
participants will be pre-screened for eligibility criteria and referred to study research assistants who will 
use the study screening form to assess potentially eligible patients for the remainder of eligibility criteria. 
For passive recruitment, study clinicians will contact study staff directly for any patient who them deem 
might meet study criteria. 
 
E. Informed Consent 
 
If eligible, potential participants will be taken to a research office to complete the informed consent 
process. Informed consent forms have been translated into local languages, and will be conducted in 
English, Runyankole, or IsiZulu, depending on the preference of the participant, by a research assistant 
trained in ethical conduct of human research. There will be two separate informed consent forms: one for 
study procedures, and a second for permission to store laboratory specimens. During the consenting 
process, the study purpose, a protocol summary, and risks and benefits of study activities will be 
explained in detail. It will be clearly explained that choosing not to enroll will have no effect on clinical 
care. After completion of the consent forms, the potential participant will be given time to ask questions 
and consider their interest in joining before signing. Those who decline participation will be referred 
back to the clinic and continue with standard clinic practice, but will be eligible to enroll in the study at a 
later time if they remain eligible. 
 
F. Enrollment of Pregnant Women 
 
Pregnant women in case at HIV clinics that also offer antenatal HIV services will be eligible for enrollment 
in this study. Their inclusion will be critical to ensure that study results are generalizable to this 
population, who stand to gain as much if not more from studies intended to elucidate optimal strategies 
of HIV care. To ensure safeguarding of pregnant women and their fetuses, procedures will be slightly 
altered for this population. First, to confirm pregnancy status, women under 50 years of age will undergo 
urine β-human chorionic gonadotropin (HCG) testing at the enrollment visit. Those who test positive will 
be referred to antenatal care in addition to the remainder of study procedures. Additionally, pregnant 
women in the standard of care arm will have a slightly altered visit schedule, such that they will return in 
1 month after study enrollment for a repeat viral load test (as opposed to 2-3 months). This 
recommendation is in keeping with South African Prevention of Mother-to-Child Transmission Guidelines 
[27], and is intended to maximize chances of viral re-suppression prior to delivery. 
 
 

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EligibilityCriteria
-HIV+on irst-lineARTforaminimumof5months
-NopriorPIexposure
-Nopriorresistancetesting
-HIV-1RNA>1,000copies/mLinlast90days
Visit1
-Randomization
-Adherencecounseling
-Resistancetestingforthoseinthe
experimentalarmonly
Visit2A-SOC
-Repeatviralload
measurement
Visit2-RT
-Reviewresistancetestresults
-Switchtosecond-linetherapy
ifresistanceispresent;
otherwise,continue irst-line
therapy
Visit2B-SOC
-Reviewviralload
measurement
-Switchtosecond-linetherapy
ifHIV-1RNA>1,000copies/
mL;otherwise,continue irst-
linetherapy
Visit3
-Outcomeassessment:
Repeatviralload
measurementand
resistancegenotype
Return9
monthsafter
enrollment
Returnwhen
viralloadresult
available
Returnafter2-3months
(1monthinpregnantwomen)
Returnwhenresistancetest
resultsareavailable
Return9
monthsafter
enrollment
STANDARDOFCAREARM
RESISTANCETESTINGARM
Figure2.StudySchema

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G. Randomization 
 
Consenting participants will be randomized by the REDCap randomization module to the standard of care 
(SOC) or the resistance-testing based (RT) arm (Figure 2). In brief, after screening has been completed, 
eligibility confirmed, and informed consent forms signed, a study participant is given a unique 
consecutive identification number in REDCap. The randomization field is selected, and the research 
assistant is informed which arm the participant has been selected for by the application. Randomization 
will be in blocks of 4 and stratified by study site, pregnancy, and duration of time since ART initiation 
(less than versus greater than one year). Randomization will be stratified by ART duration because of the 
potential heterogeneity in resistance rates between those with early treatment failure from primary drug 
resistance versus late failure due to acquired drug resistance. Strategy allocation will be unblinded to 
participants or clinic staff. 
 
V. STUDY PROCEDURES FOR PARTICIPANTS RANDOMIZED TO STANDARD OF CARE ARM 
 
A. Visit 1-SOC: Baseline Visit for Standard of Care Participants 
 
At Study Visit 1, participants randomized to the SOC will complete the baseline questionnaire to collect 
sociodemographic, HIV clinical and treatment history, self-reported ART medication adherence [28], 
quality of life [29-31], and resource allocation data. Study staff will review participant records to collect 
data on clinic initiation start date, opportunistic infection history, ART initiation date, ART regimen 
history, CD4 count and viral load result histories. A single 10cc blood specimen will be drawn for storage 
for future testing for viral load, resistance testing, and drug therapeutic monitoring (See Table 3 – Page 
18). A voided urine specimen will also be collected for future testing for therapeutic drug monitoring. 
Participants will be referred to clinic counselors who will conduct adherence support counseling as per 
standard clinical procedures. A follow-up study visit will be scheduled 2-3 months from the baseline date 
(depending on the local clinic policy), with the exception of pregnant women, who will be asked to return 
in approximately 1 month. Any interim clinical visits that are indicated by the clinic staff will be 
maintained. The participant will be instructed to continue their current ART regimen until at least the 
next clinical visit.  
 
B. Visit 2A-SOC: Repeat Viral Load Testing Visit 
 
At Study Visit 2A, participants in the SOC arm will undergo blood collection for viral load testing in 
keeping with WHO guidelines. An additional tube 10cc tube will be drawn for storage for future testing 
for viral load, resistance testing, and drug therapeutic monitoring. A voided urine specimen will also be 
collected for future testing for therapeutic drug monitoring A study questionnaire will be administered to 
assess self-reported ART medication adherence. No other procedures are scheduled at this visit. 
Participants will be notified that study staff will contact them as soon as their results are available, to 
request return to clinic for further management. The participant will be instructed to continue their 
current ART regimen until at least the next clinical visit. As soon as the viral load result is available, study 
participants will be contacted by phone and requested to return to clinic for review. If the viral load is 
indeterminate or not completed for any reason, study staff will request that the participant return for a 
repeat viral load test. 
 
 
 

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Table 2. Summary of study procedures 
Study Arm 
Visit 
Blood 
Collection 
Study Forms 
Other Procedures/Forms 
Standard of 
Care Arm 
Visit 1-SOC 
10 cc EDTA 
-Baseline questionnaire 
-Tracking form 
-Adherence questionnaire 
-Quality of life (EQ5D) 
-Resource use questionnaire 
-Staff resource use 
-ART and laboratory history 
-Adherence counseling 
-Collection of a voided urine 
specimen 
 
Visit 2A-SOC 
4 cc EDTA + 
10 cc EDTA 
-Staff resource use 
-Adherence questionnaire 
-Viral load test 
-Collection of a voided urine 
specimen 
Visit 2B-SOC 
None 
-Staff resource use 
-Review viral load results 
-Adherence counseling 
Visit 3 
4cc EDTA + 
10cc EDTA 
-Adherence questionnaire 
-Quality of life (EQ5D) 
-Resource use follow-up 
-Staff resource use 
-Interim ART and laboratory 
history 
-Viral load test, with reflex 
resistance testing if detectable 
-Collection of a voided urine 
specimen 
Resistance 
Testing Arm 
Visit 1-RT 
4cc EDTA + 
10cc EDTA 
-Baseline questionnaire 
-Tracking form 
-Adherence questionnaire 
-Quality of life (EQ5D) 
-Resource use questionnaire 
-Staff resource use 
-ART and laboratory history 
-Adherence counseling 
-Resistance test 
-Collection of a voided urine 
specimen 
Visit 2-RT 
None 
-Staff resource use 
 
-Review resistance test results  
-Adherence counseling 
Visit 3 
4cc EDTA + 
10cc EDTA 
-Adherence questionnaire 
-Quality of life (EQ5D) 
-Resource use follow-up 
-Staff resource use 
-Interim ART and laboratory 
history 
-Viral load test, with reflex 
resistance testing if detectable 
-Collection of a voided urine 
specimen  
 
C. Visit 2B-SOC: Viral Load Testing Results and Therapeutic Management 
 
At Study Visit 2B, study clinicians will review the viral load result. Participants with a viral load ≤ 1,000 
copies/mL will continue their first-line (NNRTI-based) ART regimen without change. Participants with a 
viral load >1,000 copies/mL will change ART regimen to a second-line, protease inhibitor (PI)-based or, if 
available, integrase inhibitor (II)-based therapy. Clinicians will also be encouraged to change the 
nucleos(t)ide reverse transcriptase component of the regimen (for example, changing from zidovudine to 
tenofovir), based on prior exposures, as well as WHO and national guidelines. All regimen decisions will 
be made by the study clinician, in cooperation with clinic staff at the study sites. In the case of complex 

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management issues, the site principal investigators (Dr. Winnie Muyindike in Mbarara and Dr. Yunus 
Moosa in Durban) will be contacted to offer input. At the conclusion of Visit 2B-SOC, participants in the 
SOC arm will be scheduled for a final study visit approximately 9 months after enrollment. A final visit at 
this time is chosen to allow ample time for drug suppression for participants with detectable viral load, 
and to ensure balance in observation time between study arms. Non-study clinical visits for routine 
clinical care and adherence counseling recommendations will continue in the interim as determined and 
scheduled by clinic staff. 
 
D. Visit 3: Outcome Assessment 
 
At Study Visit 3, participants will undergo repeat blood testing for plasma viral load and, if the viral load 
is detectable, reflex resistance testing will be performed. An additional 10cc tube will be drawn for 
storage for future testing for viral load, resistance testing, and drug therapeutic monitoring. A voided 
urine specimen will also be collected for future testing for therapeutic drug monitoring. A study 
questionnaire will be administered to assess resource allocation, ART medication adherence, and quality 
of life. Study staff will review participant records to update interim CD4 count, viral load, and ART 
regimen data. Results of viral load and resistance testing from this visit will be immediately made 
available to clinic staff for further patient management. At the conclusion of Visit 3, study procedures will 
be complete. 
 
E. Missing and Late Appointments 
 
If study participants do not present for study visits, study staff will call them to encourage return to clinic 
for continuation or completion of procedures. For participants who do not return within 7 days of a 
scheduled visit and unreachable by phone, a study staff member will attempt to track them at home using 
a standardized lost-to-follow-up form and procedures developed and used successfully both for program 
and clinical care in Mbarara for over 10 years [32, 33]. If participants are located, study staff will encourage 
them to return to clinic to complete procedures and/or conduct the blood draw and questionnaire in in 
the field if the participant agrees.  
 
During the COVID-19 pandemic, participants who do not present for regularly-scheduled HIV clinic 
appointments will be phoned when contact information is available. Rather than tracking at home for 
participants that cannot be reached, tracking will be delayed until the COVID-19 pandemic subsides and 
regularly scheduled study procedures can resume. 
 
VI. STUDY PROCEDURES FOR PARTICIPANTS RANDOMIZED TO RESISTANCE TESTING ARM 
 
A. Visit 1-RT: Baseline Visit for Resistance Testing Participants 
 
At Study Visit 1, participants randomized to the RT will complete the baseline questionnaire to collect 
sociodemographic, HIV clinical and treatment history, self-reported ART medication adherence, quality of 
life, and resource allocation data. Study staff will review participant records to collect data on clinic 
initiation start date, opportunistic infection history, ART initiation date, ART regimen history, CD4 count 
and viral load result histories. Upon completion of the baseline questionnaire, participants will undergo 
phlebotomy for resistance testing. Participants will be notified that study staff will contact them as soon 
as their results are available, to request return to clinic for further management. A voided urine specimen 
will also be collected for future testing for therapeutic drug monitoring. Upon completion of the study 
procedures, participants will be referred to clinic counselors who will conduct adherence support 

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counseling as per standard clinical procedures. The participant will be instructed to continue their 
current ART regimen until at least the next clinical visit. When the resistance test result is available, study 
participants will be contacted by phone and requested to return to clinic for review. 
 
B. Visit 2-RT: Resistance Testing Results and Therapeutic Management 
 
At Study Visit 2-RT, study clinicians will review the resistance testing result. A study HIV-1 RNA drug 
resistance interpretation guide will be used to help guide decision-making. Participants without 
significant drug resistance, as determined by the study clinician in consultation with the resistance 
interpretation guide and, if needed, study investigators will continue their first-line (NNRTI-based) ART 
regimen without change. Participants will be referred to clinic counselors for adherence support. 
Participants with meaningful therapeutic drug resistance will change ART regimen to a second-line, 
protease inhibitor (PI)-based or, if available, integrase inhibitor (II)-based therapy. Clinicians will also be 
encouraged to change the nucleos(t)ide reverse transcriptase component of the regimen (for example, 
changing from zidovudine to tenofovir). All regimen decisions will be made by the study clinician, in 
cooperation with clinic staff at the study sites. In the case of complex management issues, the site 
principal investigators (Dr. Winnie Muyindike in Mbarara and Dr. Yunus Moosa in Durban) will be 
contacted to offer input. At the conclusion of Visit 2-RT, participants will be scheduled for a final study 
visit approximately 9 months later. A final visit 9 months later is chosen to match the approximate 9-
month study duration for participants in the SOC arm. Non-study clinical visits for routine clinical care 
will continue in the interim as determined and scheduled by clinic staff. 
 
C. Visit 3: Outcome Assessment 
 
At Study Visit 3, participants will undergo repeat blood testing for plasma viral load and, if the viral load 
is detectable, reflex resistance testing will be performed. An additional 10cc tube will be drawn for 
storage for future testing for viral load, resistance testing, and drug therapeutic monitoring. A voided 
urine specimen will also be collected for future testing for therapeutic drug monitoring. A study 
questionnaire will be administered to assess resource allocation and quality of life. Study staff will review 
participant records to update interim CD4 count, viral load, and ART regimen data. Results of viral load 
and resistance testing from this visit will be immediately made available to clinic staff for further patient 
management. At the conclusion of Visit 3, study procedures will be complete. 
 
For participants whose visits are affected by the COVID-19 pandemic, study staff will administer study 
questionnaires via phone call where participant phone contact information is available, rather than in-
person study visits. In these cases, instead of collecting study specimens (urine and blood) during the 
study visit, alternative arrangements will be made that do not put study staff at risk. REVAMP study staff 
will work with HIV clinic staff who are already in the clinic to collect these specimens during the 
participants’ regularly scheduled HIV clinic visits if they occur during the Visit 3 follow-up window. No 
participants will be asked to come to the study site on days that they are not already scheduled to come 
to the clinic for routine appointments. For participants who cannot be reached by phone and/or if they 
do not attend clinic during the period of the COVID-19 pandemic, their study visits may fall outside of the 
Visit 3 timeline, and a study closure visit will be conducted as soon as possible once the COVID-19 
pandemic subsides. 
 
 
D. Missing and Late Appointments 
 

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If study participants do not present for study visits, study staff will call them to encourage return to clinic 
for continuation or completion of procedures. For participants who do not return within 7 days of a 
scheduled visit and unreachable by phone, a study staff member will attempt to track them at home using 
a standardized lost-to-follow-up form and procedures developed and used successfully both for program 
and clinical care in Mbarara for over 10 years [32, 33]. If participants are located, study staff will encourage 
them to return to clinic to complete procedures and/or conduct the blood draw and questionnaire in in 
the field if the participant agrees.  
 
During the COVID-19 pandemic, participants who do not present for regularly-scheduled HIV clinic 
appointments will be phoned when contact information is available. Rather than tracking at home for 
participants that cannot be reached, tracking will be delayed until the COVID-19 pandemic subsides and 
regularly scheduled study procedures can resume. 
 
VII. COVID Study Amendment 
 
We made the following provisions to account for the COVID-19 epidemic period. Study enrollment is 
complete and no new participants will be enrolled. Additionally, all study-specific visits have been 
cancelled in both Uganda and South Africa during this period, until such time that local regulations and 
authorities recommend for the resumption of non-essential activities. In the interim we will take the 
following steps in each country : 
 
1. In Uganda, REVAMP study staff will work with HIV clinic staff who are already in the clinic to 
collect these specimens during the participants’ regularly scheduled HIV clinic visits if they occur 
during the Visit 3 follow-up window. If participants do present to clinic for routine services, study 
staff will call them to administer study questionnaires via phone call where participant phone 
contact information is available, rather than in-person study visits. 
 
2. In South Africa, we have discussed study procedures with both clinic leadership and the local 
IRB. Both recommended continuing of procedures under the following conditions: 
 
a. Participants will be seen when attending for routine clinical care and or coming in for 
treatment collection and will not be asked to attend for study purposes.  
b. The study is reviewing participants that are potentially failing treatment and require a 
viral load test. The study will provide both viral load testing and resistance testing to those 
who have a detectable viral load per study protocol, which will advise further management 
of the participants.  
c. On presentation at the clinic patients will undergo routine screening for COVID 19 by 
clinic staff. Participants who screen positive will not be seen by research staff. Those that 
screen negative will have blood drawn by study nurses.  
d. Study funding will provide private transport to and from clinics for all study staff. No 
public transport will be used 
e. Study nurses are expected not to spend more than 10 to 15 minutes with participants 
during the study visit and will remain 2 metres away for all procedures aside from blood 
collection 
f. All study nurses have been trained on proper use of personal protective equipment and 
supplied with  masks, gloves, face shields, and hand sanitizer which they will strictly 
adhere to for all participant encounters  
 

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3. In both countries, For participants who cannot be reached by phone and/or if they do not attend 
clinic during the period of the COVID-19 pandemic, their study visits may fall outside of the Visit 3 
timeline, and a study closure visit will be conducted as soon as possible once the COVID-19 
pandemic subsides. 
 
 
 
VIII. DATA COLLECTION AND MANAGEMENT 
 
A. Sources of Data 
 
1. Screening Form. Screening forms will be completed by research assistants prior to enrollment in order 
to confirm study eligibility. 
 
2. Study questionnaires administered directly to study participants 
 
a. Sociodemographics Questionnaire at enrollment visit to collect basic age, sex, and socioeconomic 
data. 
b. EQ5D Quality of Life Questionnaire. EQ5D is a validated quality of life survey, that has been used 
both in populations with HIV infection and in sub-Saharan Africa [29-31]. This questionnaire will be 
administered at enrollment (Visit 1-SOC and Visit 1-RT) and again at Visit 3. The questionnaire 
will be instrumental in estimating cost-effectiveness of the intervention. 
c. Self-reported ART medication adherence. We will use a standardized ART medication adherence 
questionnaire, consisting of three questions about recent adherence. The questionnaire has been 
used and validated in sub-Saharan Africa, most notably in the Partners PREP study [28]. 
d. Tracking form. A form will be completed that records participants name, clinic ID number, phone 
number(s), treatment supporter, and address information. This form along with the signed 
consent form will be retained in a locked file cabinet, but data from this form will not be entered 
into the study database, in an effort to optimize data confidentiality. The form will be used to 
locate missing study participants who do not present for follow-up study visits. 
 
 
3. Resource Allocation Questionnaire collected from study clinician and study participant. At Visits 1 and 
3, research assistants will complete data on resource allocation from the participant and study staff. This 
will include costs of medical care and clinic resources. This data will be used for the Budget Impact and 
Cost-Effectiveness Analyses. 
 
4. Clinical records. Study staff will request clinical records of study participants. This will include 
participant charts and clinical, pharmacy, and/or clinical database data. 
 
a. HIV clinical history, including clinic enrollment date, ART start date, and ART regimen history 
b. Laboratory testing history including results of CD4 count, viral load testing results, and prior 
resistance testing results 
c. Data will be collected at study enrollment and at study conclusion to collect data both prior to and 
during study observation period. 
 
5. Laboratory results. Laboratory results ordered as part of the study, including viral load and resistance 
testing results will be collected from partner laboratories and entered into the study database.  Results of 

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these tests will also be provided to study participants. Because other tests of stored specimens, such as 
for drug therapeutic monitoring and next generation sequencing will be done at a later time, these results 
will not be available to participants.  
 
B. Specimen Collection, Process, Storage, and Laboratory Testing 
 
1. Laboratory Testing Summary 
 
A voided urine specimen will be collected at the visit 1, visit 2A-SOC, and visit 3. Study tests will be 
divided into major categories: 
 
a. All women under 50 will under go a urine β-HCG test at enrollment to determine pregnancy 
status and, if pregnant, determine the visit schedule for those in the SOC arm. 
b. Antiretroviral therapy drug levels  
 
 
Blood will be drawn by study or clinic phlebotomists at each visit. A single blood draw will occur at each 
visit. Study tests will be divided into three major categories: 
 
a. Viral load tests (plasma from processed whole blood collected into EDTA tubes) 
b. Resistance tests (plasma from processed whole blood collected into EDTA tubes) 
c. Antiretroviral therapy drug levels (DBS from unprocessed whole blood collected into EDTA 
tubes) 
 
Specimens will be divided into 1) those for immediate testing for protocol treatment decisions/outcome 
measurements, and 2) those to be stored for future testing. Specific processing, transport, and storage 
procedures will vary by country, based on logistics and laboratories partners in each country. 
 
2. Laboratory Partners 
 
a. Uganda: Joint Clinical Research Center. Joint Clinical Research Center (JCRC) serves as the primary HIV 
clinical laboratory for the country and has partnered with both the NIH and AIDS Clinical Trials Group to 
conduct laboratory testing for over 20 clinical studies. JCRC will conduct all viral load and resistance 
testing for study participants in Uganda. Partners for this work include Dr. Henry Mugerwa, Dr. 
Immaculate Nankya, and Dr. Abbas Lugemwa. 
 
b. South Africa: Laboratory testing in South African will be conducted at the Department of Virology 
based at Inkosi Albert Luthuli Central Hospital, which operates as an academic partnership between 
UKZN and the National Health Laboratory Services (NHLS). The laboratory employs a staff of technicians 
who conduct approximately 20,000 viral load tests each month and HIV drug resistance testing for 
clinical care and research purposes. The primary partner for this work will be Dr. Pravi Moodley, director 
of the Virology Laboratory. In addition, we will partner with Africa Health Research Institute (ARHI) 
Pharmacology Core in Durban, South Africa for a portion of the therapeutic drug monitoring tests. Urine 
specimens from the study will undergo quantification of tenofovir levels by liquid chromatography with 
tandem mass spectrometry. The primary partner for this work is Dr. John Adamson, director of the 
Pharmacology core. Specimens sent will not contain any identifiers to link outside collaborators to 
individual subjects. 
 

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c. United States: While we will attempt to conduct all testing in country, additional testing of stored 
specimens for low copy viral load assays and drug levels may be conducted in the United States if 
availability for quality controlled laboratories are not identified. Partner laboratories in the United States 
are at Harvard Medical School (Dr. Athe Tsibris and Dr. Jonathan Li, low copy viral load and high 
sensitivity resistance testing), the University of Colorado (Dr. Peter Anderson, pharmacology), the 
Unviersity of California San Francisco (Dr. Monica Gandhi, urine therapeutic drug monitoring),and 
UrSure, Inc (Giffin Daughtridge, urine therapeutic drug monitoring).[34] Study participants will undergo a 
separate informed consent process to agree to storage and future testing of their specimens and 
Materials Transfer Agreements will be reviewed and approved before transfer of any specimens out of 
country. 
 
3. Specimen Collection and Processing 
 
Please see the phlebotomy and specimen collection standard operating procedures for full details of 
specimen collection and processing procedures. In brief, a single blood draw will be performed at 
relevant study visit to collect whole blood into EDTA tubes (depending on the visit, with a maximum of 
15 cc per visit). Tubes will be labeled with pertinent study identifiers, refrigerated until transfer, and/or 
immediately transferred to the relevant laboratory (based on country) on the day of collection. 
Approximately 300uL of whole blood will first be removed from EDTA tubes to prepare 5 dried blood 
spots (~50uL/each) for future drug level testing. Dry blood spot cards will remain at room temperature 
overnight (minimum 4 hours) to allow drying, and then frozen for future testing. The remainder of the 
blood will be centrifuged to allow separation of plasma, which will be aliquoted into 1cc aliquots. 
Specimens will be divided for immediate testing or storage at -80oC. 
 
In addition, voided urine specimens will be collected at the enrollment visit, visit 2A-SOC, and visit 3. For 
women of under age 50, the urine specimen at the enrollment visit will be used for the urine β-HCG test. 
Otherwise, and for all other participants, specimen containers will be labeled with pertinent study 
identifiers, refrigerated until transfer, and/or immediately transferred to the relevant laboratory (based 
on country) on the day of collection. 1cc of the urine specimen will be aliquoted and stored at -80oC for 
future testing. Therapeutic drug monitoring will be done in South Africa by Africa Health Research 
Institute and in the United States by University of California San Francisco and UrSure, Inc.  
 
 
 

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4. Phlebotomy Schedule 
 
Table 3. Phlebotomy and Urine Collection Schedule 
Study Arm 
Visit 
Tube and 
Whole Blood 
Volume 
Specimens 
Purpose 
Standard of 
Care Arm 
Visit 1-SOC 
10 cc EDTA 
5 X 1cc plasma* 
Storage for future single copy viral load 
and minority resistance testing, and bulk 
(Sanger) resistance testing 
Dried Blood Spots^ Storage for future therapeutic drug 
monitoring 
Urine collection 
1cc voided urine 
Storage for future drug monitoring 
Visit 2A-SOC 
4 cc EDTA# 
2 X 1cc plasma 
Viral load testing for ART treatment 
allocation 
10 cc EDTA 
5 X 1cc plasma* 
Storage for future single copy viral load 
and minority resistance testing, and bulk 
(Sanger) resistance testing 
Dried Blood Spots^ Storage for future therapeutic drug 
monitoring 
 
Urine collection 
1cc voided urine 
Storage for future drug monitoring 
Visit 2B-SOC 
None 
No blood draw 
 
Visit 3 
4cc EDTA# 
2 X 1cc plasma 
Viral load and resistance testing for 
outcome assessment 
10cc EDTA 
5 X 1cc plasma* 
Storage for future single copy viral load 
and minority resistance testing, and bulk 
(Sanger) resistance testing 
Dried Blood Spots^ Storage for future therapeutic drug 
monitoring 
Urine collection 
1cc voided urine 
Storage for future drug monitoring 
Resistance 
Testing Arm 
Visit 1-RT 
4cc EDTA# 
2 X 1cc plasma 
Resistance testing for ART treatment 
allocation 
10cc EDTA 
5 X 1cc plasma* 
Storage for future single copy viral load 
and minority resistance testing, and bulk 
(Sanger) resistance testing 
Dried Blood Spots^ Storage for future therapeutic drug 
monitoring 
Urine collection 
1cc voided urine 
Storage for future drug monitoring 

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22 
Visti 2-RT 
None 
No blood draw 
 
Visit 3 
4cc EDTA# 
2 X 1cc plasma 
Viral load and resistance testing for 
outcome assessment 
10cc EDTA 
5 X 1cc plasma* 
Storage for future single copy viral load 
and minority resistance testing, and bulk 
(Sanger) resistance testing 
Dried Blood Spots^ Storage for future therapeutic drug 
monitoring 
Urine collection 
1cc voided urine 
Storage for future drug monitoring 
 
#Specimens in bold-faced font will be processed and tested immediately for study purposes. Other 
specimens will be stored for future testing. 
*10cc of whole blood will be centrifuged to prepare approximately 5cc plasma that will be stored as 5 X 
1cc aliquots. 3cc of stored plasma will be tested for low copy viral load assay and the remaining 2cc will 
be used for low copy resistance testing assays. These tests will be done at Harvard Medical School 
^Dried blood spots will be tested for antiretroviral therapy drug levels to assay for treatment adherence 
 
C. Data Management and Storage 
 
1. Paper Forms. There will be two paper forms used in the study: the Informed Consent Forms and the 
Tracking Form. Both of these two forms will be stored in locked file cabinets, in locked research offices. 
 
2. Electronic Database. The remainder of study data will be collected and uploaded into the study REDCap 
Database. REDCap is a password protected, online database application that allows for storage of study 
data on encrypted servers in the United States. The application includes features for field limits, data 
quality control, study scheduling, randomization, and real-time study monitoring. Questionnaires and 
clinical records will be completed in real-time and entered by study staff using encrypted study mobile 
tablets. The REDCap application allows for both online (real-time) data entry or, when internet service is 
not available, offline entry with syncing to the server when internet becomes available again. 
 
3. Clinical Records. Records from clinic databases may be entered directly into the database form 
participant charts or transferred electronically to the study project coordinator for upload into the study 
database. All data transfers will be done using password-protected, encrypted files, transferred using 
secure email or encrypted hard drives, and be free of specific patient identifiers including name, dates of 
birth, or address. 
 
D. Data Protection and Confidentiality 
 
Paper forms that include participant protected health information will be stored on the day of enrollment 
in participant specific folders within locked file cabinets in locked research offices. Only study staff will 
have access to the file cabinets. All other study data will be free of identifying information. Data will be 
stored on an encrypted REDCap Server hosted by Massachusetts General Hospital Research Management 
in Boston, Massachusetts. Access to the study database both on site and remotely is restricted to study 
staff and password protected. All study mobile tablets will be password protected and encrypted prior to 

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23 
study initiation. Data collected on mobile tablets will be uploaded to the server in real-time during data 
entry, or synced to the server as soon as data/Internet access becomes available if it is not during data 
entry, using the REDCap Offline Application. 
 
IX. STUDY MONITORING AND QUALITY ASSURANCE 
 
A. Staff Trainings 
 
1. Research Staff 
 
All research assistants will complete training through the CITI biomedical human subjects research 
course or a refresher course, as indicated. Only research staff fluent in the local languages (Runyankole or 
IsiZulu) will conduct informed consent and survey procedures. Study staff certified in phlebotomy will 
complete any blood collection procedures. Study staff will maintain active research ethics certification 
and attend any annual research ethics conferences as mandated by local policy at their institutions. 
 
2. Clinical Study Staff 
 
Prior to study initiation, clinical study staff will complete a training in the interpretation of HIV-1 
resistance testing results and management of virologic failure. The course will be designed and directed 
by study Co-Investigators Drs. Rajesh Gandhi, Vincent Marconi, and/or Kevin Ard and conducted at the 
study sites. The course will include a review of major non-nucleoside and nucleos(t)ide reverse 
transcriptase inhibitor mutations, second-line regimen options, drug-drug interactions, common drug 
toxicities, and a case-based learning session. 
 
B. Data Monitoring  
 
After review of the study protocol with National Institutes of Health officials, the proposed study is 
considered to present minimal risk to participants given that subjects will complete questionnaires and 
undergo routine HIV monitoring with viral load and resistance testing per standard guidelines, and no 
investigational agents or tests will be used. Therefore, we will not establish a formal Data and Safety 
Monitoring Board. The study statistician and co-investigators will meet annually to perform the following 
activities: a) review the research protocol and plans for data and safety monitoring; b) review progress of 
the trial, including analysis of data quality and timeliness; subject recruitment, randomization and 
retention; subject risk versus benefit; and other factors that may affect outcome. c) review serious and 
unexpected adverse event reports, provide commentary, and provide oversight to ensure that reports are 
relayed to individual IRBs; d) review proposed modifications to the study prior to their implementation. 
Meetings will be held every twelve months beginning in Year 2 of the study. We will also have an 
independent data monitor who will annually review blinded summaries of outcome and adverse event 
data and provide a report to study investigators on recommendations amending the study. 
 
C. Adverse and Unexpected Event Reporting 
 
To identify adverse events: (1) study clinicians will perform a clinical review at each study visit and (2) 
study staff will instruct participants to report any unexpected or severe adverse events to their assigned 
research assistant. Such a report will immediately be brought to the attention of study principal 
investigators. Any adverse events that are unanticipated (i.e. not related to standard HIV clinical care or 
thought to be directly related to study procedures) or severe (e.g. death) will be brought to the attention 

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24 
of the principal Investigator and reported to participating ethical review committees within 7 days. The 
relevant committee will determine whether it is appropriate to pause the study or alter the study 
protocol, and will provide suggestions/modifications to the study procedures as necessary. Possible 
modifications include adding adverse events to the consent form and re-consenting all study participants. 
The site principal investigator will be responsible for monitoring participant safety at each site on a 
monthly basis at regularly scheduled research meetings. They will keep a written log of all events and 
ensure that the ethical review committee is contacted when necessary. They will also keep a log of the 
outcome of committee decisions regarding adverse events and apprise the research team of any changes 
that need to occur as a result of such decisions.  
 
X. STATISTICAL CONSIDERATIONS AND ANALYSES 
 
A. Sample Size 
 
We propose to enroll and maintain a sample size of 840 patients, with approximately 420 randomized to 
each arm. This sample will enable adequate power to detect a clinically significant, 10% or greater rate of 
our primary outcome (viral load <200 copies/mL) at study conclusion in the RT arm (see below for 
power calculation). We have selected this threshold because we predict that a finding of this magnitude 
would be necessary to advocate for a change in current practice of virologic failure management. 
 
To assess our sample size calculation, we first estimated predicted rates of viral suppression in the SOC 
arm (Figure 3). To do so, we combined estimated suppression rates for those who remain on first line 
therapy and those who are switched to second line therapy, due to a persistent elevation in viral load  
>1,000 copies/mL. Multiple studies have reported that approximately 40% of people (range 27% - 59%) 
with an initial detectable viral load on first-line therapy load will re-suppress while remaining on first 
line therapy in the interim [2, 8-10]. Among those who do remain on first-line therapy, we estimate that only 
approximately 50% will remain suppressed on first-line therapy, owing to both high rates of underlying 
resistance [8], and sub-optimal adherence. Among patients in the SOC arm with persistent virologic failure 
on repeat testing who are switched to second line therapy, we expect approximately 80% will re-
suppress [35]. In summary, we predict that net re-suppression rates in the standard of care arm compiling 
those who remain on first-line therapy (20%) and those who switch to second line therapy (48%), will be 
approximately 68%. While comparative rates of re-suppression with resistance testing are unknown, we 
hypothesize that resistance testing has the potential to significantly improve viral suppression rates, 
particularly because rates of resistance at first-line failure are common in the region (65-90%) [7, 8, 36], 
and because those who are switched to a protease inhibitor-based combination regimen are highly likely 
to re-suppress [37-39].  
 

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25 
 
 
Assuming a 68% viral suppression rate in the SOC arm, using a two-sample test of binomial proportions 
with a Type I error rate of 5%, and allowing for a 5% rate of invalid tests, we compute a 69%, 88%, and 
97% power to detect a difference in suppression rates of 8, 10, and 12%, respectively (Table 3). Based on 
these estimates, we plan to enroll approximately 840 total participants into the study to allow sufficient 
power to detect a programmatically meaningful 10% superiority rate of viral suppression in the RT arm. 
 
Table 3. Sample Size Estimates 
Viral 
Suppression 
Rate in SOC Arm 
Viral 
Suppression 
Rate in RT Arm 
Difference in 
Outcome Rate 
α 
Sample Size 
(per group) 
Invalid 
Test Rate 
Power 
68% 
76% 
8% 
0.05 
420 
5% 
0.69 
68% 
78% 
10% 
0.05 
420 
5% 
0.88 
68% 
80% 
12% 
0.05 
420 
5% 
0.97 
 
B. Efficacy Analyses 
 
1. Primary Outcome of Interest 
 
Proportion of patients with a laboratory confirmed suppressed viral load, as defined by <200 copies/mL, 
at study conclusion (Visit 3). 
 
2. Rationale for Primary Outcome of Interest 
 
We have chosen this as our primary outcome to ensure a balanced outcome assessment 9 months after 
study initiation, standardization of viral load results across sites with different viral load testing 
platforms, and because it is an accepted international standard for other international studies of virologic 
suppression [39, 40]. 
 
3. Secondary Outcomes of Interest 
 
Repeat Viral Load Testing 
 
 
Repeat Viral Load <1,000 copies/mL 
Maintain on 1st Line Therapy 
 
SUPPRESSED on first-line therapy 
Figure 3. Schema of estimated outcomes for 
participants in the standard of care arm. 
 
Initial Viral Load > 1,000 copies/mL 
 
 
Repeat Viral Load >1,000 copies/mL 
Switch to 2nd Line Therapy 
 
FAILURE on first-line therapy 
SUPPRESSED on second-line therapy 
FAILURE on second-line therapy 
~40% 
~60% 
~50% 
~50% 
~80% 
~20% 
Adherence 
Counseling and 
3 Months Continued 
Therapy 
20%
48%

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26 
 
a. Proportion of patients with an undetectable viral load (below limit of detection) at study 
conclusion 
b. Proportion of patients with an undetectable viral load on first-line (NNRTI-based) therapy at 
study conclusion 
c. Proportion of patients with International AIDS Society-defined drug resistance mutations to 
their current regimen [41]. As part of this analysis, we will also evaluate for minority drug 
resistance. 
d. Total patient care costs, including diagnostic testing and ART costs for the study duration 
e. Retention in HIV clinical care at study completion 
f. 9-month mortality rate 
g. Change in health-related quality of life from baseline to 9 months 
 
4. Efficacy Analysis Plan 
 
Study data coordinators will perform routine reviews of data quality to identify unusual values and 
missing data entries. Initial analyses will include common exploratory data analyses, table construction, 
and scatterplots to assist in data quality control, randomization balance, and exploring for possible 
outliers or leverage points.  For our analysis of the primary outcome, we will use a two-sample test of 
binomial proportions to compare the proportions of participants in each arm who achieve virologic 
suppression at the study conclusion. For our primary analysis we will conduct an intention to treat 
analysis. For this analysis, any study participant without a confirmed viral load result at the 9-month 
study endpoint will be considered as having a detectable viral load (failure). In secondary analyses, we 
will conduct as-treated analyses for any study participants who do not complete resistance testing in the 
RT arm or participant who do receive resistance testing in the SOC arm, as documented by clinic records. 
We will also conduct a sensitivity analysis by censoring participants who are lost-to-follow-up during 
study procedures and do not have a recorded viral load at study conclusion. The unadjusted comparison 
of outcome rates will be followed by adjusted comparisons via logistic regression, adjusting for other 
confounding factors that may explain any heterogeneity or possibly confound assigned treatment and 
outcome, despite treatment randomization.  
 
The primary analyses will be followed by similar statistical analyses of secondary endpoints including the 
proportions suppressed on first-line therapy, rates of resistance, rates of retention in care, and the 9-
month mortality rate. We will compare health related quality of life measures within participants 
between baseline and study conclusion using paired t-tests. 
 
C. Economic Analyses 
 
1. Budget Impact Analysis  
 
The goal of this analysis it to estimate total projected costs for treatment programs, comparing the WHO 
standard of care versus a resistance-testing based approach to management of virologic failure. We will 
follow International Society of Pharmacoeconomics Outcomes Research (ISPOR) guidelines to develop 
models to determine the budget impact of adopting resistance testing in South Africa and Uganda, 
respectively [42]. We will populate each model with data provided by the clinical trial on costs of care, and 
add country-specific HIV epidemiology, demographic and expenditure data to estimate the budget impact 
of adopting resistance testing over five years for each strategy. We will build the model such that 
country-specific fields will be flexible to enable analysis with other countries, to facilitate policy planning 

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and decision-making. Results of this analysis will advise HIV program partners on the net resources 
required in each country to implement routine resistance testing over a 5-year period. 
 
2. Cost Effectiveness Analysis 
 
If the resistance testing intervention is superior or similar to the standard of care strategy, we will 
proceed with a full cost-effectiveness analysis. This analysis seeks to build upon prior analyses that have 
considered the economics of resistance testing in sub-Saharan Africa [22-24]. We will achieve this by 
incorporating primary efficacy, quality of life, and cost data from the clinical trial, and by estimating the 
cost utility of resistance testing versus standard of care by selecting quality adjusted life years (QALY) as 
our primary outcome of interest. 
 
To do so, we will develop a cost utility model in accordance with best practice recommendations for 
modeling from the ISPOR Good Research Practice Task Force [43] and will follow the guidelines set out by 
the National Institute For Health and Clinical Excellence Reference Case [44]. We will develop a decision 
tree cohort Markov Model using TreeAge (TreeAge Software, Inc., Williamston, MA) with methods similar 
to those previously described by Rosen et al in their analysis of the cost effectiveness of resistance 
testing-based management of virologic failure [23]. The outcome of interest will be the cost per QALY 
($/QALY), presented as an incremental cost-effectiveness ratio. We will populate the model for the first 9 
months with comparative efficacy, health-related quality of life (EQ5D questionnaire), and resource 
allocation data derived directly from the clinical trial. We will value health-related quality of life using the 
time trade off approach for a reference population in sub-Saharan Africa as adopted in similar HIV-
related cost-effectiveness analyses [45]. Thereafter, we will use published data on the natural history of 
HIV disease to model clinical outcomes every 6 months after study conclusion over a patient’s lifetime, 
including risk of opportunistic infections, hospitalization, quality of life and death [46-50]. 
  
We will vary the probability of each outcome by CD4 category, presence (or not) of detectable viral load 
and presence (or not) of resistance, to extrapolate cost utility (Table 7). To characterize uncertainty in 
the model, we will conduct a probabilistic sensitivity analysis (PSA), and present data as cost-
effectiveness acceptability curves and PSA plots. Convergent validity will be undertaken to compare the 
model to similarly published models on the cost effectiveness of resistance testing. Whereas results will 
be immediately relevant for the South African and Ugandan populations, the proposed structure of the 
model will be designed such that it may be used for adaptation to countries with similar health care 
contexts. Results will be presented in US dollars to inform foreign stakeholders. 
 
XI. HUMAN SUBJECTS CONSIDERATIONS 
 
A. Study Risks and Discomforts 
 
1. Risk 1: Unintended disclosure of HIV status or other confidential information. The study intends to 
minimize this risk through a number of protective measures. Participants will be enrolled directly from 
the HIV clinic and all study procedures will be performed in adjacent study offices. All interactions with 
study staff will be in the clinic or private rooms. Study sites have performed thousands of study visits in 
such a manner. If we visit participants at home to perform tracking of those lost from study, we will make 
every effort to plan the visit with the participant in advance (e.g. by cell phone), so he or she can make 
any arrangements necessary for maintaining privacy. We will also approach the home in an unmarked 
vehicle or on foot to avoid raising concerns. Study forms with identifiers (consent form and tracking 
form) will be kept in locked file cabinets, which are stored in locked research offices. To maintain data 

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confidentiality, participants will be assigned a unique identifier on study enrollment, and all study data 
will be entered on encrypted, password protected study tablets. The tablets will immediately sync study 
data to an encrypted, password protected Redcap Study Database, and only key study personnel will have 
access to the database. 
 
2. Risk 2: Discomfort or complication from phlebotomy procedures. Participants will undergo 
phlebotomy at each study visit. A trained phlebotomist will perform all blood collection using standard 
precautions. No more than 15 cc (approximately 3 teaspoons) of blood will be drawn on a single day, and 
no more than 50 cc over the course of the study period. 
 
3. Risk 3: Time Commitments, Transportation costs and other indirect costs of additional study visits. We 
will reimburse participants for the cost of transportation to study visits performed outside of standard 
clinical visits. We will also attempt to schedule study visits on the dates of previously scheduled clinical 
visits to minimize the burden of study procedures. We have attempted to minimize additional time 
required for study procedures. The longest study visit will be the enrollment visit, largely due to the 
informed consent procedures, which we estimate will take approximately 1 hour to complete, based on 
prior similar studies. Study questionnaires will take approximately 30 minutes to complete at the 
enrollment (Visit 1) and final (Visit 3) study visits. 
 
B. Potential Benefits 
 
1. Potential Benefits to Participants. Study participants will receive nominal incentives for completing the 
enrollment study visit (e.g. a meal, bar of soap and/or 1 kilogram pack of sugar, depending on the study 
site). They will also receive study incentives and/or transportation allocation consistent with local 
expectations, following the established standards with institutional review approval in each country. 
Details of these reimbursements are described in consent forms. All viral load and resistance testing 
performed as part of the study will be free for study participants – covered either as part of standard 
clinical care (as is done for viral load testing in South Africa), or if not, by the study itself. Study 
participants might benefit from additional viral load and resistance testing results performed as part of 
the study, or the input from study clinicians trained in management of virologic failure as part of the 
study protocol. All ART regimens and any other treatments or care will be provided by the partner HIV 
clinics. Finally, participants might also benefit from knowing that they are helping to improve our 
understanding of optimal management of virologic failure in sub-Saharan Africa.  
 
2. Potential Benefits to Society and Others. In Uganda, where viral load testing is not always available, the 
study will provide additional viral load testing free of charge to the study clinics to enhance screening of 
potential participants, and non-participants might benefit from this service. Results of the study might be 
of benefit to HIV infected people in the sub-Saharan African region. Over 10 million people in sub-
Saharan Africa have accessed ART over the past decade. Approximately 1 in 3 of them who remain on 
therapy will suffer virologic failure within two years of treatment initiation. Thus, understanding the 
optimal and most-cost effective method of virologic failure management will have a critical impact on 
both patients and treatment programs as viral load testing becomes more affordable and available in the 
region. 

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XII. REFERENCES 
 
1. Haberer JE, Kiwanuka J, Nansera D, Ragland K, Mellins C, Bangsberg DR. Multiple measures reveal 
antiretroviral adherence successes and challenges in HIV-infected Ugandan children. PLoS One 
2012; 7(5):e36737. 
2. Gupta RK, Goodall RL, Ranopa M, Kityo C, Munderi P, Lyagoba F, et al. High Rate of HIV 
Resuppression After Viral Failure on First-line Antiretroviral Therapy in the Absence of Switch to 
Second-line Therapy. Clin Infect Dis 2014; 58(7):1023-1026. 
3. Barth RE, van der Loeff MF, Schuurman R, Hoepelman AI, Wensing AM. Virological follow-up of adult 
patients in antiretroviral treatment programmes in sub-Saharan Africa: a systematic review. 
Lancet Infect Dis 2010; 10(3):155-166. 
4. UNAIDS. Landmark HIV diagnostic access program will save $150m and help acheive new global 
goals on HIV. Available at: 
http://www.unaids.org/en/resources/presscentre/pressreleaseandstatementarchive/2014/september/20140925prvi
ralload; Accessed 13 Dec 2014. In; 2014. 
5. Mermin J, Ekwaru JP, Were W, Degerman R, Bunnell R, Kaharuza F, et al. Utility of routine viral load, 
CD4 cell count, and clinical monitoring among adults with HIV receiving antiretroviral therapy in 
Uganda: randomised trial. Bmj 2011; 343:d6792. 
6. Marconi VC, Sunpath H, Lu Z, Gordon M, Koranteng-Apeagyei K, Hampton J, et al. Prevalence of HIV-1 
drug resistance after failure of a first highly active antiretroviral therapy regimen in KwaZulu 
Natal, South Africa. Clin Infect Dis 2008; 46(10):1589-1597. 
7. Hosseinipour MC, van Oosterhout JJ, Weigel R, Phiri S, Kamwendo D, Parkin N, et al. The public health 
approach to identify antiretroviral therapy failure: high-level nucleoside reverse transcriptase 
inhibitor resistance among Malawians failing first-line antiretroviral therapy. AIDS 2009; 
23(9):1127-1134. 
8. Hoffmann CJ, Charalambous S, Sim J, Ledwaba J, Schwikkard G, Chaisson RE, et al. Viremia, 
resuppression, and time to resistance in human immunodeficiency virus (HIV) subtype C during 
first-line antiretroviral therapy in South Africa. Clin Infect Dis 2009; 49(12):1928-1935. 
9. El-Khatib Z, Delong AK, Katzenstein D, Ekstrom AM, Ledwaba J, Mohapi L, et al. Drug resistance 
patterns and virus re-suppression among HIV-1 subtype C infected patients receiving non-
nucleoside reverse transcriptase inhibitors in South Africa. J AIDS Clin Res 2011; 2(117). 
10. Jobanputra K, Parker LA, Azih C, Okello V, Maphalala G, Kershberger B, et al. Factors associated with 
virological failure and suppression after enhanced adherence counselling, in children, 
adolescents and adults on antiretroviral therapy for HIV in Swaziland. PLoS One 2015; 
10(2):e0116144. 
11. Tuller DM, Bangsberg DR, Senkungu J, Ware NC, Emenyonu N, Weiser SD. Transportation costs 
impede sustained adherence and access to HAART in a clinic population in southwestern Uganda: 
a qualitative study. AIDS Behav 2010; 14(4):778-784. 
12. Siedner MJ, Lankowski A, Tsai AC, Muzoora C, Martin JN, Hunt PW, et al. GPS-measured distance to 
clinic, but not self-reported transportation factors, are associated with missed HIV clinic visits in 
rural Uganda. AIDS 2013; 27(9):1503-1508. 
13. Lankowski AJ, Siedner MJ, Bangsberg DR, Tsai AC. Impact of geographic and transportation-
related barriers on HIV outcomes in sub-Saharan Africa: a systematic review. AIDS and behavior 
2014; 18(7):1199-1223. 
14. Siedner MJ, Lankowski A, Haberer JE, Kembabazi A, Emenyonu N, Tsai AC, et al. Rethinking the "pre" 
in pre-therapy counseling: no benefit of additional visits prior to therapy on adherence or viremia 
in Ugandans initiating ARVs. PloS one 2012; 7(6):e39894. 

Version Date: 14th December, 2020 
   REVAMP Study: Study Protocol 
 
 
 
 
30 
15. Durant J, Clevenbergh P, Halfon P, Delgiudice P, Porsin S, Simonet P, et al. Drug-resistance 
genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet 1999; 
353(9171):2195-2199. 
16. Cohen CJ, Hunt S, Sension M, Farthing C, Conant M, Jacobson S, et al. A randomized trial assessing 
the impact of phenotypic resistance testing on antiretroviral therapy. AIDS 2002; 16(4):579-588. 
17. Tural C, Ruiz L, Holtzer C, Schapiro J, Viciana P, Gonzalez J, et al. Clinical utility of HIV-1 genotyping 
and expert advice: the Havana trial. AIDS 2002; 16(2):209-218. 
18. Haubrich RH, Kemper CA, Hellmann NS, Keiser PH, Witt MD, Tilles JG, et al. A randomized, 
prospective study of phenotype susceptibility testing versus standard of care to manage 
antiretroviral therapy: CCTG 575. AIDS 2005; 19(3):295-302. 
19. Friis-Moller N, Reiss P, Sabin CA, Weber R, Monforte A, El-Sadr W, et al. Class of antiretroviral drugs 
and the risk of myocardial infarction. N Engl J Med 2007; 356(17):1723-1735. 
20. Haberer JE, Kahane J, Kigozi I, Emenyonu N, Hunt P, Martin J, et al. Real-time adherence monitoring 
for HIV antiretroviral therapy. AIDS Behav 2010; 14(6):1340-1346. 
21. Boender ST, Hoenderboom BM, Sigaloff KC, Wellington M, Siwale M, Kityo CM, et al. Pretreatment 
HIV Drug Resistance Increases Regimen Switch in sub-Saharan Africa. Presented at 2015 
Conference on Retroviruses and Opportunistic Infections. 23-26 February, 2015. Available at: 
http://www.croiconference.org/sessions/pretreatment-hiv-drug-resistance-increases-regimen-switch-sub-
saharan-africa. Accessed 1 March 2015. 2015. 
22. Levison JH, Wood R, Scott CA, Ciaranello AL, Martinson NA, Rusu C, et al. The clinical and economic 
impact of genotype testing at first-line antiretroviral therapy failure for HIV-infected patients in 
South Africa. Clin Infect Dis 2013; 56(4):587-597. 
23. Rosen S, Long L, Sanne I, Stevens WS, Fox MP. The net cost of incorporating resistance testing into 
HIV/AIDS treatment in South Africa: a Markov model with primary data. Journal of the International 
AIDS Society 2011; 14:24. 
24. Phillips A, Cambiano V, Nakagawa F, Magubu T, Miners A, Ford D, et al. Cost-effectiveness of HIV 
drug resistance testing to inform switching to second line antiretroviral therapy in low income 
settings. PloS one 2014; 9(10):e109148. 
25. Inzaule SC, Hamers RL, Zeh CE, Rinke de Wit TF. Stringent HIV Viral Load Threshold for 
Virological Failure Using Dried Blood Spots: Is the Perfect the Enemy of the Good? Journal of 
acquired immune deficiency syndromes 2016; 71(1):e30-33. 
26. Smit PW, Sollis KA, Fiscus S, Ford N, Vitoria M, Essajee S, et al. Systematic review of the use of dried 
blood spots for monitoring HIV viral load and for early infant diagnosis. PLoS One 2014; 
9(3):e86461. 
27. National Consolidated Guidelines for the Prevention of Mother-to-Child Transmission of HIV 
(PMTCT) and the Management of HIV in Children, Adolescents and Adults. National Department of 
Health, South Africa. Available at: http://www.sahivsoc.org/upload/documents/ART Guidelines 
15052015.pdf. 2015. 
28. Musinguzi N, Muganzi CD, Boum Y, 2nd, Ronald A, Marzinke MA, Hendrix CW, et al. Comparison of 
subjective and objective adherence measures for preexposure prophylaxis against HIV infection 
among serodiscordant couples in East Africa. AIDS 2016; 30(7):1121-1129. 
29. Hughes J, Jelsma J, Maclean E, Darder M, Tinise X. The health-related quality of life of people living 
with HIV/AIDS. Disability and rehabilitation 2004; 26(6):371-376. 
30. Jelsma J, Maclean E, Hughes J, Tinise X, Darder M. An investigation into the health-related quality 
of life of individuals living with HIV who are receiving HAART. AIDS care 2005; 17(5):579-588. 
31. Louwagie GM, Bachmann MO, Meyer K, Booysen Fle R, Fairall LR, Heunis C. Highly active 
antiretroviral treatment and health related quality of life in South African adults with human 
immunodeficiency virus infection: A cross-sectional analytical study. BMC public health 2007; 7:244. 

Version Date: 14th December, 2020 
   REVAMP Study: Study Protocol 
 
 
 
 
31 
32. Geng EH, Emenyonu N, Bwana MB, Glidden DV, Martin JN. Sampling-based approach to 
determining outcomes of patients lost to follow-up in antiretroviral therapy scale-up programs in 
Africa. JAMA 2008; 300(5):506-507. 
33. Geng EH, Glidden DV, Emenyonu N, Musinguzi N, Bwana MB, Neilands TB, et al. Tracking a sample of 
patients lost to follow-up has a major impact on understanding determinants of survival in HIV-
infected patients on antiretroviral therapy in Africa. Trop Med Int Health 2010; 15 Suppl 1:63-69. 
34. Koenig HC, Mounzer K, Daughtridge GW, Sloan CE, Lalley-Chareczko L, Moorthy GS, et al. Urine assay 
for tenofovir to monitor adherence in real time to tenofovir disoproxil fumarate/emtricitabine as 
pre-exposure prophylaxis. HIV Med 2017; 18(6):412-418. 
35. Gilks CF, Walker AS, Dunn DT, Gibb DM, Kikaire B, Reid A, et al. Lopinavir/ritonavir monotherapy 
after 24 weeks of second-line antiretroviral therapy in Africa: a randomized controlled trial 
(SARA). Antiviral therapy 2012; 17(7):1363-1373. 
36. Sunpath H, Wu B, Gordon M, Hampton J, Johnson B, Moosa MY, et al. High rate of K65R for 
antiretroviral therapy-naive patients with subtype C HIV infection failing a tenofovir-containing 
first-line regimen. AIDS 2012; 26(13):1679-1684. 
37. Ciaffi L, Koulla-Shiro S, Sawadogo A, Moing VL, Eymard-Duvernay S, Izard S, et al. Efficacy and safety 
of three second-line antiretroviral regimens in HIV-infected patients in Africa. AIDS 2015; 29:1473-
1481. 
38. Bartlett JA, Ribaudo HJ, Wallis CL, Aga E, Katzenstein DA, Stevens WS, et al. Lopinavir/ritonavir 
monotherapy after virologic failure of first-line antiretroviral therapy in resource-limited 
settings. AIDS 2012; 26(11):1345-1354. 
39. Paton NI, Kityo C, Hoppe A, Reid A, Kambugu A, Lugemwa A, et al. Assessment of second-line 
antiretroviral regimens for HIV therapy in Africa. N Engl J Med 2014; 371(3):234-247. 
40. Dart Trial Team. Virological response to a triple nucleoside/nucleotide analogue regimen over 
48 weeks in HIV-1-infected adults in Africa. AIDS 2006; 20(10):1391-1399. 
41. Wensing AM, Calvez V, Gunthard HF, Johnson VA, Paredes R, Pillay D, et al. 2014 Update of the drug 
resistance mutations in HIV-1. Topics in antiviral medicine 2014; 22(3):642-650. 
42. Mauskopf JA, Sullivan SD, Annemans L, Caro J, Mullins CD, Nuijten M, et al. Principles of good 
practice for budget impact analysis: report of the ISPOR Task Force on good research practices--
budget impact analysis. Value in health : the journal of the International Society for Pharmacoeconomics 
and Outcomes Research 2007; 10(5):336-347. 
43. Caro JJ, Briggs AH, Siebert U, Kuntz KM, Force I-SMGRPT. Modeling good research practices--
overview: a report of the ISPOR-SMDM Modeling Good Research Practices Task Force--1. Value in 
health : the journal of the International Society for Pharmacoeconomics and Outcomes Research 2012; 
15(6):796-803. 
44. Weidle PJ, Malamba S, Mwebaze R, Sozi C, Rukundo G, Downing R, et al. Assessment of a pilot 
antiretroviral drug therapy programme in Uganda: patients' response, survival, and drug 
resistance. Lancet 2002; 360(9326):34-40. 
45. Cleary SM, McIntyre D, Boulle AM. The cost-effectiveness of antiretroviral treatment in 
Khayelitsha, South Africa--a primary data analysis. Cost effectiveness and resource allocation : C/E 
2006; 4:20. 
46. Mellors JW, Munoz A, Giorgi JV, Margolick JB, Tassoni CJ, Gupta P, et al. Plasma viral load and CD4+ 
lymphocytes as prognostic markers of HIV-1 infection. Annals of internal medicine 1997; 
126(12):946-954. 
47. Luz PM, Morris BL, Grinsztejn B, Freedberg KA, Veloso VG, Walensky RP, et al. Cost-effectiveness of 
genotype testing for primary resistance in Brazil. Journal of acquired immune deficiency syndromes 
2015; 68(2):152-161. 

Version Date: 14th December, 2020 
   REVAMP Study: Study Protocol 
 
 
 
 
32 
48. Schackman BR, Goldie SJ, Freedberg KA, Losina E, Brazier J, Weinstein MC. Comparison of health 
state utilities using community and patient preference weights derived from a survey of patients 
with HIV/AIDS. Medical decision making : an international journal of the Society for Medical Decision 
Making 2002; 22(1):27-38. 
49. Holtgrave DR, Pinkerton SD. Updates of cost of illness and quality of life estimates for use in 
economic evaluations of HIV prevention programs. Journal of acquired immune deficiency syndromes 
and human retrovirology : official publication of the International Retrovirology Association 1997; 
16(1):54-62. 
50. Robberstad B, Olsen JA. The health related quality of life of people living with HIV/AIDS in sub-
Saharan Africa - a literature review and focus group study. Cost effectiveness and resource allocation : 
C/E 2010; 8:5.