Modulating the Impact of Critical Events in Early HIV Infection: Effect of ART Initiation and Alcohol Use
Phase: NA
Conditions: HIV Infection
Sponsor: Fred Hutchinson Cancer Center

Modulating the impact of Critical Events during Early HIV Infection: Effect of ART Initiation and 
Alcohol Use 
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Modulating the Impact of Critical Events in Early HIV Infection: Effect of ART 
Initiation and Alcohol use 
The MERLIN Study 
Sponsored by: 
National Institute on Drug Abuse (NIDA) 
U. S. National Institutes of Health (NIH) 
Protocol Chair and Principal Investigator 
Ann Duerr, M.D., Ph.D., M.P.H. 
Fred Hutchinson Cancer Research Center 
Seattle, WA, United States 
Protocol Co-Chair 
Javier Lama, M.D., M.P.H. 
Asociacion Civil Impacta Salud y Educacion 
Lima, Peru 
Version 3.0  
April 12, 2018 
IRO REC'D 01/20/ 2021
FHCRC IRB Approval  
FEB 11 2021 
Document Released Date

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Contents 
PROTOCOL TEAM ........................................................................................................................ 6 
1.1 PROTOCOL TEAM ROSTER ............................................................................................... 6 
1.1.1 Fred Hutchinson Cancer Research Center.................................................................... 6 
1.1.2 Asociación Civil Impacta Salud y Educación ................................................................. 6 
1.1.3 University of California, San Francisco .......................................................................... 7 
1.1.4 Université de Montréal ................................................................................................... 8 
1.1.5 University of Washington ............................................................................................... 8 
1.1.6 Blood Systems Research Institute ................................................................................. 9 
1.1.7 Yale University ................................................................................................................ 9 
1.1.8 University of North Carolina ........................................................................................... 9 
1.1.9 National Institute on Drug Abuse, U.S National Institutes of Health ............................. 9 
1.2 CLINICAL LABORATORIES ............................................................................................... 10 
1.3 RESEARCH FACILITIES .................................................................................................... 10 
1.4  INSTITUTIONAL REVIEW BOARDS ................................................................................ 10 
SIGNATURE PAGE...................................................................................................................... 11 
EXECUTIVE SUMMARY .............................................................................................................. 12 
Treatment Regimen: .............................................................................................................. 14 
BACKGROUND ............................................................................................................................ 15 
4.1 INTRODUCTION ................................................................................................................. 15 
4.2 JUSTIFICATION.................................................................................................................. 16 
4.2.1 Timing of ART Initiation and Progression of HIV Disease ........................................... 17 
4.2.2 Microbial Translocation, GI Microbiome, and Inflammation in HIV Disease ............... 17 
4.2.3 Alcohol Effects on Microbial Translocation and the GI Microbiome ............................ 17 
4.2.4 Alcohol Use, Systemic Inflammation, and Immunity ................................................... 17 
4.2.5 Effect of Alcohol on HIV Progression is Unclear ......................................................... 18 
4.2.6 HIV Integration Sites .................................................................................................... 18 
4.2.7 Neurocognitive Impairment .......................................................................................... 18 
4.3 PROBLEM UNDER INVESTIGATION .................................................................................. 19 
5. HYPOTHESIS ........................................................................................................................... 20 
6. OBJECTIVES ........................................................................................................................... 20 

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6.1 PRIMARY OBJECTIVES .................................................................................................... 20 
6.2 SECONDARY OBJECTIVES .............................................................................................. 21 
7. STUDY DESIGN ....................................................................................................................... 21 
7.1 GENERAL STUDY DESIGN ............................................................................................... 21 
7.2  MANAGEMENT OF SUBJECTS WITH VIROLOGIC FAILURE OR PREMATURE 
DISCONTINUATION OF TREATMENT ................................................................................... 23 
8. SELECTION AND ENROLLMENT OF SUBJECTS ............................................................... 23 
8.1 DESCRIPTION OF THE POPULATION ............................................................................. 23 
8.1.1 Inclusion Criteria ........................................................................................................... 23 
8.1.2 Exclusion Criteria ......................................................................................................... 24 
8.2 RECRUITMENT .................................................................................................................. 25 
9. STUDY TREATMENT .............................................................................................................. 25 
9.1 Treatment REGIMENS........................................................................................................ 25 
9.2 Administration ...................................................................................................................... 27 
9.3 Duration ............................................................................................................................... 27 
9.4 STUDY Product Formulation and Preparation ................................................................... 27 
9.5 Product Supply .................................................................................................................... 27 
9.6 Pharmacy Facilities ............................................................................................................. 27 
9.7 Drug Inventory ..................................................................................................................... 28 
9.8 Drug Dispensing .................................................................................................................. 28 
9.9 Concomitant Medications .................................................................................................... 28 
9.9.1 Precautions with Concomitant Medications ................................................................. 28 
9.9.2 Prohibited Medications ................................................................................................. 28 
9.9.3 Options for Medication Substitutions Due to Intolerance/Toxicity ............................... 29 
9.9.4 Options for Medication Substitutions for Virologic Failure ........................................... 29 
9.10 Adherence Assessment .................................................................................................... 30 
10. STUDY PROCEDURES ......................................................................................................... 30 
10.2 Recruitment ....................................................................................................................... 34 
10.2.1 SABES 3 Participants................................................................................................. 34 
10.2.2 New participants with acute infection ......................................................................... 34 
10.3 Timing of Visits .................................................................................................................. 34 
10.3.1 Enrollment Assessments ............................................................................................ 34 
10.3.2. Follow-up Assessments ............................................................................................ 35 
10.3.3 Last study visit ............................................................................................................ 35 
10.3.4  Definitions of evaluations and special indications .................................................... 35 

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11.WARNINGS AND PRECAUTIONS ........................................................................................ 40 
11.1 Lactic Acidosis/Severe Hepatomegaly with Steatosis ...................................................... 40 
11.2 Patients with HIV and HBV Coinfection ............................................................................ 40 
11.3 New Onset or Worsening Renal Impairment .................................................................... 40 
11.4 Liver Enzymes ................................................................................................................... 41 
11.5 Fat Redistribution .............................................................................................................. 41 
11.6 Immune Reconstitution Syndrome.................................................................................... 41 
11.7 Co-Administration with Related Drugs .............................................................................. 42 
12. MANAGEMENT OF TOXICITIES .......................................................................................... 42 
12.1 CLINICAL TOXICITIES ..................................................................................................... 42 
12.1.1 Nausea and Vomiting ................................................................................................. 42 
12.1.2 Diarrhea ...................................................................................................................... 42 
12.1.3 Symptomatic Hyperlactatemia ................................................................................... 43 
12.2 LABORATORY TOXICITIES ............................................................................................ 43 
12.2.1 Increases in Values for Liver Function Tests ............................................................. 44 
12.2.2 Lipase ......................................................................................................................... 44 
12.2.3 Triglycerides/Cholesterol ............................................................................................ 45 
12.2.4 Hyperglycemia ............................................................................................................ 45 
12.2.5 Renal Insufficiency ..................................................................................................... 46 
12.2.6 Hypophosphatemia .................................................................................................... 46 
12.3 all other Grade 3 or 4 Toxicity ........................................................................................... 46 
13. CRITERIA FOR DISCONTINUATION ................................................................................... 47 
13.1 PREMATURE STUDY DISCONTINUATION ................................................................... 47 
13.2 PERMANENT TREATMENT DISCONTINUATION ......................................................... 47 
13.3 ASSURING REPORTING OF SUSPENSION TO THE CLINICAL TRIAL ...................... 47 
14. STATISTICAL CONSIDERATIONS ...................................................................................... 48 
14.1. Primary Objectives ........................................................................................................... 48 
14.2 Secondary Objectives ....................................................................................................... 48 
14.3 ENDPOINTS ..................................................................................................................... 48 
14.3.1 Primary Endpoints ...................................................................................................... 48 
14.3.2 Secondary Endpoints ................................................................................................. 49 
14.4 SAMPLE SIZE AND ACCRUAL .......................................................................................... 49 
14.4.1 Merlin Cohort of Acute and Recent HIV Infection ......................................................... 49 
14.4.2 MERLIN Sub-studies ..................................................................................................... 49 
14.5 MONITORING....................................................................................................................... 49 

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14.6 ANALYSES .......................................................................................................................... 49 
14.6.1 Testing of Urine, and Dried Blood Spots ....................................................................... 50 
14.6.2 Measurement of the HIV Reservoir ............................................................................... 50 
14.6.3 Innate Immune Responses and Inflammation ............................................................... 51 
14.6.4 Dysbiosis of the Gut Microbiota and Correlation with Markers of HIV-Associated 
Immunopathology. ..................................................................................................................... 51 
14.6.5 DNA Integration Sites .................................................................................................... 52 
14.6.6 Neurologic and Neurocognitive Effects ......................................................................... 52 
15. DATA COLLECTION, MONITORING, AND ADVERSE EXPERIENCE REPORTING ....... 52 
15.1 Data Collection .................................................................................................................. 52 
15.2 DEFINITION OF AN ADVERSE EVENT .......................................................................... 53 
15.3 GOVERNANCE ................................................................................................................. 53 
15.4 ASSESSMENT OF AE RELATIONSHIP TO STUDY AGENT......................................... 53 
15.5 FOLLOW-UP OF ADVERSE EVENTS ............................................................................. 54 
15.6 EXPEDITED ADVERSE EVENTS REPORTING TO NATIONAL INSTITUTE OF DRUG 
ABUSE....................................................................................................................................... 54 
15.6.1 Study Agents for Expedited Reporting to National Institute on Drug Abuse Program 
Official .................................................................................................................................... 54 
15.6.2 Grading Severity of Events ........................................................................................ 54 
15.6.3 Adverse Events Reporting Periods ............................................................................ 54 
15.7 CONTACT FOR QUESTIONS ABOUT EXPEDITED ADVERSE EVENTS .................... 55 
15.8 SOCIAL ADVERSE EVENTS ........................................................................................... 55 
16. HUMAN SUBJECTS PROTECTION ..................................................................................... 55 
16.1 INSTITUTIONAL REVIEW BOARDS AND ETHICS COMMiTTEE REVIEW .................. 55 
16.2 SUBJECT CONFIDENTIALITY ........................................................................................ 55 
16.3 STUDY DISCONTINUATION ........................................................................................... 55 
17. PUBLICATIONS OF RESEARCH FINDINGS ....................................................................... 56 
18 REFERENCES ........................................................................................................................ 57 
 
 
 
 
 
 
 
 
 
 

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PROTOCOL TEAM  
 
1.1 PROTOCOL TEAM ROSTER 
1.1.1 Fred Hutchinson Cancer Research Center 
 
Ann Duerr, MD, PhD, MPH 
Principal Investigator and Protocol Chair 
Director (Scientific Affairs), HIV Vaccine Trials Network Member, Vaccine and Infectious Disease 
& Public Health Science Divisions, Fred Hutchinson Cancer Research Center 
Affiliate Professor, Departments of Global Health and Epidemiology, University of Washington, 
Seattle, WA 
Mailstop E2-112, FHCRC 
1100 Fairview Ave N 
Seattle WA 98109 
Phone: +1-206-667-7938 
e-mail: aduerr@fredhutch.org 
 
Rachel Bender Ignacio, MD, MPH 
Investigator and Safety Monitor 
Research Associate 
Vaccine and Infectious Diseases Division 
Fred Hutchinson Cancer Research Center 
Mailstop E2-112-FHCRC 
1100 Fairview Ave N 
Seattle WA 98109 
Phone: +1-206-667-4628 
e-mail: rbenderi@fredhutch.org 
 
Delia Pinto-Santini, PhD 
Project Coordinator 
Duerr Clinical Trials: Peru HIV Studies 
Mailstop E2-112, FHCRC 
1100 Fairview Ave N 
Seattle WA 98109 
Fred Hutchinson Cancer Research Center, Seattle, WA 
Phone: +1-206-667-7858 
e-mail address: psantini@fhcrc.org   
 
1.1.2 Asociación Civil Impacta Salud y Educación 
 
Javier R. Lama, MD, MPH 
Protocol Co-Chair, Site Principal Investigator IMPACTA San Miguel 
Director, HIV Prevention Studies, IMPACTA PERU Clinical Trials Unit 
Asociacion Civil Impacta Salud y Educacion 
Affiliated Assistant Professor, University of Washington Department of Global Health 
Av. Almirante Miguel Grau No. 1010. Lima 4, Peru 
Phone: +51-1-206-7800 Ext 407 
e-mail address: jrlama@impactaperu.org 

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Martin Llancare, PharmD 
Protocol Pharmacist  
IMPACTA PERU Clinical Trials Unit 
Asociacion Civil Impacta Salud y Educacion 
Av. Almirante Miguel Grau No. 1010. Lima 4, Peru 
Phone: +51-1-206-7800 Ext 316 
e-mail address: mllancare@impactaperu.org 
 
Jessica Rios, CNM. 
Study Coordinator 
IMPACTA PERU Clinical Trials Unit 
Asociacion Civil Impacta Salud y Educacion 
Av. Almirante Miguel Grau No. 1010. Lima 4, Peru. 
Phone: +51-1-206-7800 Ext 210 
e-mail address: jrios@impactaperu.org 
 
Karin Sosa, CNM 
Research Assistant 
IMPACTA PERU Clinical Trials Unit 
Asociacion Civil Impacta Salud y Educacion 
Av. Almirante Miguel Grau No. 1010. Lima 4, Peru. 
Phone: +51-1-206-7800 Ext 210 
e-mail address: ksosa@impactaperu.org 
 
1.1.3 University of California, San Francisco 
 
Peter Hunt, MD 
Associate Professor 
Department of Medicine 
1001 Potrero Ave 
San Francisco CA 94110 
Phone:  +1415-206-8165 
Email address: peter.hunt@ucsf.edu 
 
Susan Lynch PhD 
Associate Professor of Medicine 
Director Colitis and Crohn's Disease Microbiome Research Core, 
Division of Gastroenterology,  
UCSF 
513 Parnassus Ave, Med Sci 
San Francisco, CA 94112 
Phone: 415-476-6784 
email:  susan.lynch@ucsf.edu 
 
Jeffrey Milush, PhD 
Assistant Professor of Medicine 
UCSF 

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1001 Potrero Ave 
San Francisco, CA 94110 
Phone:  415-206-3881 
email:  Jeffrey.milush@ucsf.edu 
 
Christopher Pilcher, MD 
Professor of Medicine 
UCSF Medical School 
1001 Potrero Ave 
San Francisco CA 94110 
Phone: 415-476-4082x403 
email: chris.pilcher@ucsf.edu 
 
1.1.4 Université de Montréal 
 
Nicolas Chomont, PhD 
Assistant Professor,  
Département de microbiologie, infectiologie et immunologie,  
Université de Montréal  
Montreal, Quebec 
Canada 
Phone: 514 890-8000 ext. 31266 
email: nicolas.chomont@umontreal.ca  
 
1.1.5 University of Washington 
 
Lisa Frenkel, MD 
Professor  
University of Washington,  
Department of Pediatrics Children's Hospital & Medical Center,  
Box 359300/8G-1 
Seattle, WA 98195 
United States of America 
Phone: 206 469-6661 
 
email: lfrenkel@uw.edu  
 
James Mullins, PhD 
Professor 
Departments of Microbiology, Medicine and Laboratory Medicine 
University of Washington 
Rosen Building, Box 358070 
1959 NE Pacific St. 
Seattle WA 98195 
Phone: (206) 732-6163 
Email: jmullins@uw.edu 

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1.1.6 Blood Systems Research Institute 
 
Sheila Keating, PhD 
Scientist II 
Head, Core Immunology Laboratory 
Blood Systems Research Institute 
270 Masonic Avenue 
San Francisco, CA 94118 
Phone: 415-749-6606 x499 
email:skeating@bloodsystems.org 
 
1.1.7 Yale University 
 
Serena Spudich MD MA 
Professor of Neurology 
Division Chief, Neurological Infections and Global Neurology 
Yale  
PO Box 208018 
New Haven, CT 06520 
Phone: 203-688-5303 
email: serena.spudich@yale.edu 
 
1.1.8 University of North Carolina 
 
Kevin Robertson, PhD 
Director of Neuropsychology Center, AIDS Dementia Center 
170 Manning Drive 
CB#7025 
Chapel Hill, NC 27599 
email: robertson.kevin@unc.edu 
 
1.1.9 National Institute on Drug Abuse, U.S National Institutes of Health 
 
William Aklin, Ph.D. 
Project Officer 
National Institute on Drug Abuse 
6001 Executive Boulevard,  
Bethesda, MD 20892  
e-mail addressjkhalsa@nida.nih.gov 
e-mail address: aklinwm@mail.nih.gov  
 
Redonna Chandler, Ph.D. 
Director, Health Services Branch 
National Institute on Drug Abuse 
6001 Executive Boulevard,  
Bethesda, MD 20892   
e-mail address: rchandle@nida.nih.gov  

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1.2 CLINICAL LABORATORIES 
IMPACTA PERU Clinical Trials Unit Central Laboratory 
Carmela Ganoza, MD 
Av. Almirante Miguel Grau No. 1010. Lima 4, Peru 
Phone: +51-1-206-7800 Ext 306 
e-mail address: cganoza@impactaperu.org 
 
University of Washington Molecular Genetics Laboratory 
Dr. James Mullins 
Rosen Building, Box 358070 
1959 NE Pacific St. 
Seattle WA 98195 
Phone: +1-206-732-6163 
e-mail address: jmullins@uw.edu  
 
1.3 RESEARCH FACILITIES 
IMPACTA San Miguel Clinical Research Site 
Asociacion Civil Impacta Salud y Educacion 
Jr. Putumayo No. 177. Lima 32, Peru 
Phone: +51-1-562-1600 
 
IMPACTA Barranco Clinical Research Site 
Asociacion Civil Impacta Salud y Educacion 
Av. Almirante Miguel Grau No. 1010. Lima 4, Peru 
Phone: +51-1-206-7800 
 
1.4  INSTITUTIONAL REVIEW BOARDS 
Fred Hutchinson Cancer Research Center Institutional Review Board 
Institutional Review Office 
PO Box 19024, J6-110 
Seattle, WA 98109-1024 
Tel: +1-206-667-5900 
e-mail address: jsutherl@fhcrc.org  
 
Comité Institucional de Bioética 
Asociación Civil Impacta Salud y Educación 
Phone: +51-1-206-7800 Ext 318 
e-mail address: etica@impactaperu.org 
 
 
 

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SIGNATURE PAGE 
 
Modulating the Impact of Critical Events in Early HIV Infection: Effect of ART Initiation 
and Alcohol use 
 
Sponsored by: 
 
National Institute on Drug Abuse (NIDA) 
U. S. National Institutes of Health (NIH) 
 
I, the Principal Investigator, agree to conduct this study in full accordance with the provisions of 
this protocol.  I will comply with all requirements regarding the obligations of investigators.  I also 
agree to maintain all study documentation for at least two years. 
 
I have read and understand the information in the Investigator's Brochures and/or package 
inserts, including the potential risks and side effects of the products under investigation, and will 
ensure that all associates, colleagues, and employees assisting in the conduct of the study are 
informed about the obligations incurred by their contribution to the study. 
 
 
 
 
 
Ann Duerr, MD, PhD, MPH 
Principal Investigator and Protocol Chair 
 
 
 
____________________________   
__________________________ 
Signature of Principal Investigator 
 
 
 
Date 
 
 
 

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EXECUTIVE SUMMARY 
 
Protocol Title: Modulating the Impact of Critical Events in Early HIV Infection: Effect of ART 
Initiation and Alcohol use 
 
Short Protocol Title: The MERLIN Study 
 
Sites: IMPACTA San Miguel and Barranco Clinical Research Sites at IMPACTA PERU Clinical 
Trials Unit in Lima, Peru.  
 
Planned Starting Date: January 2017 
 
Planned Ending Date: December 2022 
 
Study Rationale: This study will investigate the relative long-term benefit of early initiation of 
antiretroviral therapy (ART) in men who have sex with men (MSM) and transgender women (TW) 
with recently-acquired HIV infection.  The impact of early ART initiation will be assessed in 
participants according to their Fiebig stage at diagnosis.  Fiebig staging uses the presence of HIV 
RNA, p24 and patterns of antibodies bands seen on western blots to define 5 stages during the 
first 3-4 months after HIV acquisition plus a 6th stage for long-term infection.   
 
The overall objective is to determine the impact of time of ART initiation and high-level alcohol 
use on a number of HIV-related clinical parameters. These include time to viral suppression, CD4 
count, HIV reservoir, changes in the gut microbiome and neurocognitive functioning. 
 
Primary Objectives: 
 
1) To determine the relative long-term benefits of immediate vs. early vs. delayed (by 6 
months) initiation of ART.  
 
2) To determine the impact of high-level alcohol use on the relative long-term benefits of 
immediate vs. early vs. delayed ART initiation   
 
Primary Endpoints (1): 
 
1) Measure the impact of early treatment on cell-activation, and inflammation by comparing 
cellular markers of inflammation in study participants who initiated treatment at varying 
times after HIV acquisition.   
 
2) Measure the impact of early treatment on the replication-competent HIV reservoir (size of 
the reservoir and types of cells involved) in study participants who initiated treatment at 
varying times after HIV acquisition.   
 
3) Determine whether early ART initiation prevents long-term changes in gastrointestinal 
tract bacterial microbiota and correlate these changes with systemic markers of 
inflammation and disease progression such as the activity of the kynurenine pathway of 
tryptophan catabolism and plasma concentrations of the inflammatory cytokine 
interleukin-6 (IL-6). 

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4) Document the impact of early ART initiation on ‘non-HIV-associated’ diseases such as 
neurocognitive disorders.  Assess the correlation of these clinical outcomes with 
laboratory markers of cell activation, inflammation and HIV reservoir size and 
characteristics. 
 
5) Determine the impact of high-level alcohol use on the outcomes listed in 1-4, after 
controlling for time of ART initiation. 
 
Primary Endpoints (2): 
 
1) Examine the time course of seeding of the replication-competent HIV reservoir quantifying 
the size of the reservoir and identifying the types of cells involved at time-points close to 
HIV acquisition. 
 
2) Characterize innate immune responses (cytokines and other soluble mediators) shortly 
after infection and determine the impact of these responses on the strength and character 
of the subsequent adaptive immune response to HIV, as well as the size and 
characteristics of the HIV reservoir (see above). 
 
3) Probe changes in gastrointestinal tract bacterial microbiota shortly after HIV infection and 
determine the correlation of these changes with two established markers of disease 
progression: the activity of the kynurenine pathway of tryptophan catabolism and plasma 
concentrations of the inflammatory cytokine interleukin-6 (IL-6). 
 
Design: The MERLIN Study extends the follow-up of participants enrolled in the SABES Study, 
a study of ~250 MSM and TW in Lima with acute and recent HIV infection enrolled in an early vs. 
deferred antiretroviral treatment study. The MERLIN study will offer follow-up to all of the patients 
enrolled in the SABES study, prioritizing the participants who also were enrolled in a related 
Observational Study, in which baseline peripheral blood mononuclear cell (PBMC) isolation 
sampling was conducted.  Additionally to the participants previously enrolled in SABES,  up to 25 
additional participants with acute HIV diagnosis will be enrolled directly in this study and will be 
treated immediately upon diagnosis.   
 
Consenting eighteen-year old or older MSM and TW, who participated and received ART in the 
SABES Study and who have acceptable hematologic, liver, and renal function will be considered 
to participate in the MERLIN study, in which they will continue a 3-drug ART regimen.  
 
Because of the low number of participants, which acute infection who received immediate 
treatment in the SABES study and who could be eligible for MERLIN, a new enrollment and follow-
up cohort will be open with up to 25 participants (see above).  In this cohort, participants with 
acute HIV infection will initiate antiretroviral treatment immediately after receiving diagnosis and 
will also be followed up for an extended time.  
 
Duration: Up to 5 years from enrollment on this protocol (through 2022) with visits timed 
referencing date of HIV diagnosis and original Sabes study visits (or SABES enrollment if 
applicable. 
 

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Treatment Regimen:   
 
In SABES Step 3, participants had been randomized to either one of the following arms: 
Immediate Arm: to immediately receive ART for 48 weeks; or Deferred Arm: to delay treatment 
for 24 weeks (unless Peruvian criteria for initiation of treatment are met), and then receive ART 
at 24 weeks.  
 
For the purposes of correlative studies, participants in the Immediate Arm are further categorized 
as initiating Immediate ART (in Acute HIV: Fiebig I/II) or Early ART (Recent HIV: Fiebig III/V) 
infection.   
 
The MERLIN participants will initiate the co-formulation EVG/COBI/FTC/TDF (Genvoya) for its 
component TAF.  
 
 EVG/COBI/FTC/TDF is not readily available in private or public sector HIV care in Peru, but it is 
considered acceptable based on FDA-approval and US-based HIV guidelines to the Peruvian 
Ministry of Health (MOH).   
 
Participants receiving protease-inhibitor (PI)-based regimens at MERLIN enrollment will be 
transitioned to Genvoya after individual evaluation.   
 
 
• 
Group A:  This group will be comprised of persons who initiated EFV/FTC/TDF during 
SABES Step 3.   
 
These participants will continue with EVG/COBI/FTC/TAF. 
 
• 
Group B:  This group will be comprised of persons who initiated EFV/FTC/TDF during 
SABES Step 3 and completed all 48 weeks of the protocol before MERLIN (or the 
Observational Study) began enrollment.  
 
These participants were transferred to continue their in the MOH/TARGA (Peruvian 
Government) HIV clinics and received non-study first-line ART (EFV + lamivudine (3TC) 
+ zidovudine (AZT), or other regimen) after completing SABES Step 3 and up to their 
enrollment in the MERLIN study.  
 
These participants will continue treatment with EVG/COBI/FTC/TAF. 
 
• 
Group C: This group will be comprised of persons who initiated EVG/COBI/FTC/TDF 
during SABES Step 3 or other persons currently taking a PI or INSTI-based regimens.  
Because INSTI-based regimens are considered preferential as described above, at 
MERLIN enrollment, these participants will be transferred to EVG/COBI/FTC/TAF. 
Persons who require to take PI-based regimens have generally had EFV 
intolerance/hypersensitivity or even virologic resistance.  For these reasons, they cannot 
receive other treatments. All persons receiving PI-based regimens will also be 
transitioned to EVG/COBI/FTC/TAF unless a clinical contraindication exists.  
 
• 
Group D:  This group will consist of participants who were diagnosed with acute infection 

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and enrolled in MERLIN  immediately after their diagnosis and who will initiate 
antiretroviral treatment immediately with EVF/COV/FTC/TAF.   
 
Evaluations: All participants will be evaluated at regular intervals for primary and secondary 
outcomes. 
 
BACKGROUND 
 
4.1 INTRODUCTION  
Recent data suggest that initiation of antiretroviral therapy very early after HIV acquisition can 
confer several benefits.  These include reduction in the size of the HIV reservoir and decrease in 
HIV-associated systemic inflammation that has been linked to non-AIDS mortality in HIV-infected 
participants, even when HIV replication is effectively controlled by antiretroviral therapy (ART).  In 
addition, some patients who are treated very early appear to effectively control HIV replication 
years later when ART is discontinued, sometimes referred to as a functional cure.  However, very 
early initiation of ART (in Fiebig stages I or II [FI or FII] prior to seroconversion) does not prevent 
the establishment of HIV reservoirs, which eventually expand in most patients when ART is 
discontinued [1, 2]. Early ART initiation is, nonetheless, associated with preservation of CD4+ T 
cells, preserving normal gut microbiota, averting a major driver of HIV-related immune activation, 
and limiting the size of the HIV reservoir [3]. When, by contrast, ART is initiated after 
seroconversion (in Fiebig stage III [FIII] or later), many HIV-associated changes have already 
occurred, including seeding of HIV reservoirs, damage to GI mucosa, and initiation of 
inflammatory cascades [3]. Some if not all of these effects may be related to the development of 
dysbiosis (a markedly different composition of the gut microbiota that might itself drive continued 
inflammation). 
 
Since ART initiation within weeks of HIV acquisition is not a viable public health strategy, it is 
important to more completely understand the relative long-term benefits of initiating ART at very 
early times after infection (FI-II) as opposed to after a short (during FIII-V) or longer delay (at 24 
weeks). Because most HIV-infected individuals come to medical attention long after they have 
been infected, data on individuals with known infection dates, especially those who were infected 
very recently, is a valuable resource.  The MERLIN study of HIV-infected (HIV+) participants will 
allow the collection and analysis of clinical data and biologic specimens at multiple time points 
from HIV+ participants with known infection dates in Lima.  It will focus on studies of HIV clinical 
course which incorporate data on time of infection, duration of infection prior to initiation of 
antiretroviral therapy (ART), and molecular markers of infection such as inflammation and immune 
dysfunction (including innate immune responses), size and location of HIV reservoirs, and 
changes in the microbiome.  In addition, it will follow participants clinically, with collection of data 
such as CD4 count, neurocognitive function etc. The effects of alcohol on microbial translocation 
and pro-inflammatory cytokines are not unlike early changes after HIV infection [4-6]; however, 
alcohol’s role in HIV pathogenesis and progression is not well defined. Since the possibility that 
high-level alcohol use can mitigate the benefits of early ART is emerging as a potentially important 
public health issue, the MERLIN study will evaluate the impact of alcohol use as well as time of 
ART initiation on HIV pathogenesis in Peruvian MSM and TGW in whom high-level alcohol use is 
common. 
 
The overarching hypotheses of the MERLIN study are as follows: 1. Initiation of ART soon after 
HIV infection will dampen perturbations of GI microbiota, reduce HIV-induced inflammatory 

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changes, and decrease seeding of the reservoir. Initiation of ART in FI-II will have the greatest 
benefit. CD4 counts and peripheral inflammatory markers in the FIII-V group and the group treated 
at 24 weeks will approach those in the FI-II group at 1.5 and 3.5 years after ART initiation; in 
contrast, changes in the GI microbiome and the HIV reservoir over time will be more modest. 2. 
Irrespective of the time of ART initiation, alcohol use will compound the negative effects of HIV to 
generate greater levels of dysbiosis, microbial translocation, up-regulation of inflammatory 
pathways, and seeding of the HIV reservoir. 
 
Specimens from the SABES and MERLIN studies will be used for a series of laboratory 
investigations probing the mechanisms by which early treatment reduces the HIV reservoir and 
HIV-associated inflammation, and seeking to determine how soon after HIV acquisition ART must 
be initiated to confer these beneficial effects. The most in-depth studies will prioritize participants 
enrolled during the latter half of the SABES study who had large PMBC collections at the time of 
HIV diagnosis and throughout follow-up. These include the following 3 groups based on time of 
ART initiation: a) Immediate: during FI-II (N~20), b) Early: during FIII-V (N~35) or c) Deferred: at 
24 weeks after diagnosis (N~55).  A small number of additional studies may be conducted on all 
participants in the SABES study: a) Immediate: during FI-II (N~35), b) Early: during FIII-V (N~72) 
or c) Deferred: at 24 weeks after diagnosis (N~115).  The MERLIN study will assess outcomes 
after 1.5 and 3.5 years after initiation of ART in these MSM and TGW. The results will be evaluated 
every 6 months during the follow-up of the participants in the study (up to the end of 2022). 
Laboratory analyses will be conducted in Lima, Perú and Seattle, WA as well as in the laboratories 
of our collaborators at University of California, San Francisco (UCSF) and University of Montreal 
(UoM). Additional neuropsychiatric and biologic data will be collected to evaluate neuro-
inflammation and cognitive changes in early HIV infection (collaborators at UCSF, Yale, and 
UNC). 
 
4.2 JUSTIFICATION 
 
Early ART initiation is associated with preservation of CD4+ T cells, reduced immune activation 
(lower levels of CD4+ and CD8+ T cell activation and lower soluble inflammatory markers), lower 
total HIV DNA levels, and lower cell-associated RNA levels [7]. Recent studies suggest that very 
early initiation of ART (prior to seroconversion in humans or before detection of viremia in non-
human primates) does not prevent the establishment of HIV reservoirs, which eventually expand 
when ART is discontinued [2, 8]. However, early initiation of ART prevents loss of gut Th17 cells 
thereby reducing HIV-related immune activation and limits the size of the HIV reservoir [1, 3]. 
Drug and/or alcohol use in North and South American MSM is associated with increased risk of 
acquiring and transmitting HIV, and we hypothesize it will influence the course of HIV infection as 
well. In Peru, where we have enrolled a cohort of MSM/TGW with acute or recent HIV infection, 
alcohol use is common. In a recent study, 52% of Peruvian MSM reported alcohol use during sex 
while only 5% reported concomitant drug use. MSM from the US participating in the same study 
reported drug and alcohol use of 39% and 38%, respectively [9]. A 2011 survey of 5,148 gay and 
bisexual men in 5 Peruvian cities reported alcohol use disorder (AUD), defined as a score ≥8 on 
the Alcohol Use Disorder Identification Test (AUDIT), in 63% of respondents [10, 11], five times 
higher than that reported by males in the general Peruvian population [12]. 
 

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4.2.1 Timing of ART Initiation and Progression of HIV Disease 
 
Even in the setting of suppressive ART, persistent elevations in T cell activation and systemic 
inflammation appear to play a central role in HIV disease progression. Early ART initiation is 
associated with lower levels of CD4+ and CD8+ T cell activation, lower total HIV DNA levels, and 
lower cell-associated RNA levels in subjects with virologic suppression [7]. In a small number of 
individuals who were treated very early and then stopped ART, viral suppression continues off 
therapy [13-15]. Six months of ART initiated shortly after seroconversion (during FIII) improved 
many immune parameters, although not to the level seen when ART is initiated prior to 
seroconversion (during FI-II) which resulted in near normal (HIV-uninfected) levels for some 
parameters [3]. These results raise the question of how to translate these findings to a clinical 
setting. Recent studies suggest that initiation of ART during hyper-acute infection (i.e., Fiebig 
stages I and II) may be optimal, but detecting such individuals and linking them rapidly to care 
pose substantial logistical challenges.  
 
4.2.2 Microbial Translocation, GI Microbiome, and Inflammation in HIV Disease 
 
The GI mucosa is involved in HIV-induced inflammation directly through microbial translocation, 
which results in increased levels of circulating LPS [16], and indirectly through up-regulation of 
inflammatory responses in dendritic cells in response to IFN-γ and HIV Tat and Nef. This in turn 
has detrimental effects on Th17 cells in the gut mucosa [17, 18], leading to impairment of mucosal 
integrity. Alterations in the gastrointestinal (GI) microbiome, called dysbiosis, also contribute to 
these inflammatory processes [19, 20]. Dysbiotic bacteria enriched in HIV infection produce 
tryptophan catabolites (e.g., of the kynurenine pathway) which are linked to inflammation and 
have been associated with translocation of microbial products into the systemic circulation [21, 
22]. Thus, the bacterial communities in HIV-infected individuals may be important drivers of the 
inflammatory processes that contribute to disease. Importantly, effective ART does not completely 
reverse the immunopathologic changes in GI mucosa in all subjects, raising the possibility that 
differences among ART-treated subjects may be related to whether ART was initiated prior to 
‘irreversible’ establishment of dysbiotic GI microbial communities. 
 
4.2.3 Alcohol Effects on Microbial Translocation and the GI Microbiome 
 
Importantly for this protocol, alcohol use has also been linked to microbial translocation and 
increased levels of endotoxins, such as lipopolysaccharide (LPS), in the portal and systemic 
circulation. Binge drinking in healthy individuals with no history of AUD results in significant, rapid, 
and transient increases in serum LPS and 16S rDNA, as well as lipoprotein binding protein(LBP) 
and soluble CD14 (sCD14) [23], likely due to microbial translocation from the gut to the circulation.  
Gut microbiome shifts in AUD include reductions in the normally dominant species and 
enrichment of Gammaproteobacteria and depletion of Bacteroidetes [4], two taxa that are similarly 
altered in the gut of HIV-infected subjects and linked with HIV disease progression [19, 21, 22]. 
Thus, alcohol use may exacerbate microbial translocation, inflammation and HIV disease 
progression by inducing qualitative and/or quantitative changes in these microbial communities. 
 
4.2.4 Alcohol Use, Systemic Inflammation, and Immunity 
 
Innate immune responses appear to initiate the inflammatory cascade linked to alcohol use in 
animals and in humans [24]. Chronic alcohol consumption has been linked to increases in 

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circulating levels of LPS,  the pro-inflammatory cytokines [5], and acute-phase proteins [6]. These 
changes are likely mediated at least in part by microbial translocation: thus, microbial pathogen-
associated molecular patterns interact with host receptors and trigger downstream transcription 
and expression of inflammatory genes. Alcohol may also interfere with granulocyte and monocyte 
production [25], impair the function of dendritic and phagocytic cells [26] and decrease natural 
killer (NK) cell activity [27].  
 
4.2.5 Effect of Alcohol on HIV Progression is Unclear 
 
There is substantial overlap between the effects of alcohol and HIV on microbial translocation, 
changes in GI flora, and systemic inflammation. Indeed, some in vitro and animal studies link 
alcohol use to higher plasma HIV/SIV RNA viral loads (VL) [28] and accelerated progression of 
SIV disease [29], although this finding has not been replicated in all studies [30]. Human studies 
of alcohol and HIV infection report mixed results; some small studies suggest poorer outcomes 
[31, 32] while larger cohort studies found no effect on VL or CD4+ T cell counts in ART-naïve or 
treated patients [33]. The differences may be due to unmeasured confounders, poor ART 
adherence among treated patients, and/or inaccurate assessment of alcohol use (e.g., due to 
single or widely-spaced measurements, social desirability bias, and use of non-standard 
definitions). Regardless, the aforementioned detrimental effects of alcohol on microbiome 
composition, microbial translocation, and systemic inflammation suggest that it may exacerbate 
HIV disease, and that treatment of AUD in the context of HIV infection may help to resolve 
inflammation and diminish the viral reservoir. 
 
4.2.6 HIV Integration Sites  
 
Recent studies of individuals who initiated ART during chronic infection [34, 35] indicate that HIV 
integration into genes associated with cancer or cell cycle regulation confers a survival advantage 
to specific cells, apparently the result of increased proliferation and formation of clonal populations 
that persist during suppressive ART. Identifying which early integration events lead to proliferation 
and persistence of infected cells may suggest novel interventions to reduce or clear the HIV 
reservoir that is limited in size due to early ART. We expect that participants who initiate ART 
early vs. later after primary infection will have fewer unique integration sites prior to initiation of 
ART and at 18 and 42 months will have fewer proviruses in genes associated with cancer and 
cell proliferation. Also, we expect that AUD will correlate with T cell activation and inflammatory 
markers. Therefore, we hypothesize that individuals with low alcohol use will have relatively fewer 
unique integration sites at all time-points compared to those with high use who initiate ART at the 
same Fiebig stage, and at 18 and 42 months will have fewer proviruses in genes associated with 
cancer and cell proliferation. 
 
4.2.7 Neurocognitive Impairment 
 
HIV-associated neurocognitive disorders (HAND) are caused by the impact of HIV infection on 
the central nervous system (CNS). HIV infection of the CNS is associated with neuronal damage, 
inflammation and, in approximately 40% of treated individuals, cognitive impairment [36-38].Both 
CNS pathology and cognitive impairment can persist despite antiretroviral therapy (ART) when it 
is initiated during established HIV infection; and cognitive impairment may associate with 
persistent HIV replication and HIV-driven inflammation in the CNS. One intriguing possibility is 
that CNS HIV persistence may be reduced by very early initiation of ART. In collaborative studies 

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of individuals treated immediately with acute HIV infection in Thailand [41, 42], we have shown 
that key markers of inflammation in the CNS quickly normalize  and that cognitive function remains 
normal over the first 6 months of longitudinal follow-up[43]. Among HIV-infected individuals in the 
US, we found that those initiating ART earlier in the first year of HIV infection (i.e., during “recent” 
HIV infection) had significantly better cognitive function after a year of ART than did those in whom 
treatment was more delayed. These observational data strongly suggest—but do not prove—that 
there is some window in the first year of infection (i.e., during acute and/or recent infection) during 
which ART can keep HIV from developing the ability to replicate efficiently and persist locally in 
the CNS on ART. Both alcohol and stimulant use can augment systemic inflammation, increase 
local neuroinflammation and cause direct neuronal injury. Alcohol-induced neurotoxicity overlaps 
with HIV mechanisms of neuropathogenesis through oxidative stress, overproduction of pro-
inflammatory factors, impairment of blood–brain barrier and glutamate associated neurotoxicity 
[44].  Thus, it is possible that higher psychostimulant and alcohol use can lead to accelerated or 
less reversible neurologic and neurocognitive effects.   
 
Collectively, these results suggest that alcohol may compound the negative effects of HIV to 
generate greater levels of dysbiosis, microbial translocation, up-regulation of inflammatory 
pathways and seeding of the HIV reservoir. They also suggest that initiation of ART soon after 
HIV infection might: 1) dampen perturbations of GI microbiota, 2) reduce HIV-induced 
inflammatory changes, and 3) decrease seeding of the reservoir, although to a lesser degree in 
those with AUD. We will explore these questions in MSM/TGW (N~240) with acute or recent HIV 
infection, a large proportion of whom report high-level alcohol use. The proposed research will be 
conducted in MERLIN, as an extension of our ongoing study of acute and recent HIV infection 
among 
MSM/TGW 
in 
Peru, 
entitled 
the 
‘SABES’ 
study. 
(https://clinicaltrials.gov/ct2/show/NCT01815580?term=SABES&rank=1). 
 
4.3 PROBLEM UNDER INVESTIGATION 
 
Results of several recent studies suggest that initiation of ART soon after HIV infection can reduce 
HIV-induced inflammatory changes and seeding of the reservoir. Clinical studies also suggest 
that early initiation of therapy can have a beneficial impact by reducing the HIV-associated 
morbidity that persists even when HIV replication is successfully achieved through ART.  These 
studies leave open the question of how soon after HIV acquisition ART must be initiated to achieve 
these beneficial results. While initiation of ART during hyper-acute (Fiebig stages I and II) might 
seem optimal, detecting such individuals and linking them rapidly to care poses huge logistical 
challenges, not the least of which is instituting more wide spread screening for HIV infection using 
NAAT (nucleic acid amplification test). The intent of this study is to determine the impact of early 
treatment initiation among patients with acute (HIV RNA+/ seronegative) or very recent (HIV 
seropositive with a documented HIV RNA tested within the past 3 months) HIV infection. Most 
participants in this study participated in the SABES study (see below) and initiated ART early after 
HIV acquisition. Because participants were randomized to start ART at different times, the 
proposed studies will allow assessment of the relative impact of ART initiated at various times 
during the first year of infection. In addition, a small number of participants with chronic HIV 
infection and a small number of HIV-uninfected participants will be enrolled for comparison.   
 
 

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5. HYPOTHESIS 
 
ART initiation during FI-II stages will largely prevent changes in GI microbiota and inflammatory 
markers, and reduce the size of the reservoir of replication-competent HIV.  
 
1) Over time CD4 counts and peripheral inflammatory markers in seropositive participants 
who initiate ART 2 to 8 months after infection (ie in the Early and Deferred Arms) will 
approach those who initiated ART during Acute (FI-II) HIV; in contrast, we expect that 
these individuals initiating ART subsequent to acute infection will demonstrate persistent 
changes in the GI microbiome and in the HIV reservoir.  
 
2) High-level alcohol use will compound the negative effects of HIV to generate greater levels 
of dysbiosis, microbial translocation, and up-regulation of inflammatory pathways, leading 
to increased seeding of the HIV reservoir prior to ART initiation. Early treatment should 
diminish, but not completely prevent, the changes in the microbiome associated with 
alcohol consumption and their impact on immune activation and seeding of the HIV 
reservoir. 
 
 
6. OBJECTIVES 
 
The overall objective is to determine the impact of time of ART initiation and high-level alcohol 
use on a number of HIV-related clinical parameters. These include time to viral suppression, CD4 
count, HIV reservoir, changes in the gut microbiome and neurocognitive functioning. 
 
6.1 PRIMARY OBJECTIVES 
 
1) To determine the relative long-term benefits of immediate vs. early vs. deferred initiation 
of ART. 
 
Initiation of ART during Fiebig I-II, while theoretically appealing, is currently infeasible in 
clinical practice because the duration of FI-II is very short (10 days) and because antibody-
based tests, used almost world-wide, are unable to diagnose FI-II. Six months of ART 
initiated shortly after seroconversion (FIII) can improve many immune parameters, 
although not to the near normal level seen when ART is initiated during FI-II [3]. Longer-
term follow-up of seropositive participants who started ART ~2-8 months after HIV 
acquisition compared to those initiating ART during FI-II is needed to see whether markers 
of inflammation and residual viral load might continue to improve after 6 months, 
decreasing the difference between the groups. Methods: We will evaluate the 3 groups 
using specimens from equivalent times after ART initiation through the first 5 years of ART 
usage, comparing CD4 counts, time to undetectable VL, GI microbiota, and inflammatory 
markers. The size of the replication-competent HIV reservoir in PBMCs will be compared 
using measurements of multiply spliced viral RNA (msRNA) and the degree of low-level 
infection of new cells by assessing the production of circular viral DNA (2LTR HIV DNA). 
We will model the size and persistence of the viral reservoir across all ART-adherent study 
participants. In a subset of individuals from each group, the proviral integration sites will 

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be defined at ART initiation and after 1.5 and 3.5 years to assess the maintenance of the 
reservoir by proliferating CD4 cells. We will continue evaluating endpoints annually or 
biannually, as long as participants remain on study. 
 
2) To determine the impact of high-level alcohol use on the relative long-term benefits of 
immediate vs. early vs. delayed ART initiation   
 
Dysbiosis is present in individuals with high-level alcohol use [23, 24, 27, 45-47] and in many 
HIV-infected patients. The extent of dysbiosis correlates with established markers of HIV 
disease progression and the consequent inflammatory processes contribute to HIV disease 
progression, even in treated individuals. Methods:  We will use monthly self-report data on 
alcohol use as well as alcohol biomarkers in blood and hair to assess alcohol consumption as 
a continuous, time-varying predictor. In all participants at the time of diagnosis, and at multiple 
time points prior to ART in those enrolled into the deferred group, we will assess VL, GI 
microbiota, pro-inflammatory cytokines, and HIV reservoirs. We will compare these factors 
between subjects by their reported alcohol use, focusing on events occurring shortly after HIV 
acquisition. Specimens from uninfected and chronically infected subjects are available as 
controls. Finally, among ART-adherent subjects with persistent viral suppression, we will HIV 
DNA integration sites in those with and without high-level alcohol use at 1.5 and 3.5 years 
after ART initiation. 
 
 
 
6.2 SECONDARY OBJECTIVES 
1) To estimate the impact of time of initiation of antiretroviral therapy on short- and long-term 
clinical and laboratory outcomes. 
 
2) To evaluate the correlation between gastrointestinal dysbiosis and systemic immune activation 
in MSM with HIV and alcohol use disorders. 
 
3) To evaluate the association with alcohol abuse and timing on ART initiation neurocognitive 
function and neuro inflammation in MSM with acute and recent HIV. 
 
4) To determine whether NNRTI and INSTI-based ART regimens have differential effects on time 
to HIV VL suppression and size of the latent HIV reservoir. 
 
5) To determine whether NNRTI and INSTI-based ART have differential moderation of immune 
activation associated with HIV and alcohol abuse. 
 
7. STUDY DESIGN 
 
7.1 GENERAL STUDY DESIGN 
 
This protocol for the MERLIN study describes the extended follow-up of participants enrolled in 
the SABES study, a study of ~250 HIV+ MSM and TGW in Lima, Perú. In this study, we will enroll 
up to 25 individuals with acute HIV infection.   
The SABES study: The ongoing SABES study combines laboratory and epidemiologic data with 

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modeling to investigate the hypothesis that 
early ART initiation and management of 
alcohol use disorder will prevent onward 
HIV 
transmission 
among 
MSM/TGW 
diagnosed with acute (FI-FII: Ab-/HIV 
RNA+) or recent (≤3 months) HIV infection 
(FIII-V). The SABES study population is 
MSM and transgender women (TGW) not 
using feminizing hormones (all referred to 
as “MSM” from here on) in Lima. This study 
is being conducted in 3 phases: 1) HIV 
screening, 2) monthly follow-up testing of 
HIV-uninfected participants by point-of-care 
EIA and NAAT testing for HIV RNA in pools 
of seronegative specimens (pools are run 
daily), and 3) enrollment of MSM with 
incident HIV infection into a randomized 
ART treatment study (Figure 1). Only 
participants with acute (seronegative but 
HIV RNA+) or recent HIV infection (EIA+ 
with a prior HIV-negative test within 3 
months) are eligible for enrollment in the 
treatment phase of the SABES study. These participants are stratified by acute vs. recent infection 
and randomized 1:1 to Immediate arm (to receive ART immediately) or Deferred arm (to receive 
ART beginning at 24 weeks or when the participant meets Peruvian treatment initiation 
thresholds, whichever comes first) (Figure 1). We completed enrollment of 225 HIV+ participants 
into the SABES study by the end of March 2016.  A small number (5-10) of additional participants 
will be enrolled in SABES; those with symptomatic acute HIV infection will receive ART 
immediately, in accordance with current Peruvian treatment guidelines and will therefore not be 
randomized to possibly delay ART.  The Human Subjects section contains a discussion of risks 
and benefits. All SABES participants received either EFV/FTC/TDF or EVG/COBI/FTC/TDF as 
first line medication. Virologic suppression at 48 and 96 weeks is equivalent for both regimens 
when used as initial treatment [48]; however because EVG/COBI/FTC/TDF may result in more 
rapid viral suppression we began using EVG/COBI/FTC/TDF for new participants when it became 
available as a donated drug in late 2015.  
 Specimen collection: The MERLIN study involves laboratory analysis of specimens collected 
during the 48-week SABES study as well as during the MERLIN study, through 2022 (about 5 
years after MERLIN enrollment) .  Visits with specimen collection occurred in the SABES study at 
1, 2 and 4 weeks after ART initiation (study weeks 1, 2, 4 for the Immediate arm and weeks 25, 
26, 28 for the Deferred arm); additional visits occur at 8, 16, 24, 32, 40 and 48 weeks. Extensive 
samples, including blood, stool for microbiome, and dried blood spots and hair for drug and 
alcohol tests were collected at each study visit for SABES study participants, starting at participant 
number 110. In addition, during the latter half of the SABES study, neurocognitive testing was 
conducted starting at participant 110, as well as collection of cerebrospinal fluid (CSF) by lumbar 
punctures on a subset to investigate the early neurologic impact of HIV infection. For the MERLIN 
study, we will collect blood, urine, rectal secretions and rectal biopsies, and stool specimens every 
24 weeks throughout 2022, as well as additional neurocognitive testing and collection of CSF on 
a subset of participants. 
Figure 1: SABES study enrollment July 2013- 
July 2016 

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7.2 MANAGEMENT OF SUBJECTS WITH VIROLOGIC FAILURE OR PREMATURE 
DISCONTINUATION OF TREATMENT 
 
Virologic failure is defined if there is an HIV-1 RNA of >400 copies/mL in 2consecutive 
measurements after having reached an HIV-1RNA level of <50copies/mL in 2 consecutive 
measurements separated by at least 14 days. 
 
If there is a sub-optimal virologic response, the Virologic Laboratory of the University of 
Washington will perform genotyping from a sample taken from before discontinuation of the 
treatment when the HIV-1 RNA is >500 copies/ML with the goal of determining if there has been 
development of resistance or not, and if yes, to help in the selection of a new antiretroviral 
regimen.  The substituted regimen will be provided by the study while the participant is 
participating in the study.  If the genotype does not reveal evidence of resistance and there are 
convincing arguments (that is to say, adherence has improved substantially or there were 
intercurrent illnesses that could explain the elevated viral load) the participant could continue with 
the original treatment plan.  Any decision to continue with the regimen in the context of a 
suboptimal viralogic response must be discussed with the PI/co-PI of the study.  The subsequent 
management of whether or not to initiate a new regimen or modify the regimen must be at the 
discretion of the local investigator in concordance with the standard of care.  Subjects that remain 
in the study will be requested to complete all of the described evaluations during which time they 
will be provided an alternative antiretroviral treatment provided by the study. 
 
 
8. SELECTION AND ENROLLMENT OF SUBJECTS 
 
8.1 DESCRIPTION OF THE POPULATION 
Consenting MSM and TW eighteen-year old or older, who participated and received ART in the 
SABES Study; acceptable hematologic, liver, and renal function to support an approved 3-drug 
ART regimen.   
 
8.1.1 Inclusion Criteria 
 
1) Age ≥18 years 
 
2) MSM or TW 
 
3) Able to give consent, including consent for medical procedures, blood draws, and 
switching antiretroviral medication if indicated 
 
4) Participants with acute/recent HIV infection who have participated in SABES  
 
a. Current SABES participants, receiving ART in their assigned treatment by the time 
this study is implemented; or 
 
b. SABES participants who completed 48 weeks of study participation in their 

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assigned treatment arm and were rolled over into the ART program sponsored by 
the Peruvian MOH; 
 
c. Any participants of the Collaborative Observational Protocol who do not meet 
criteria for a or b above 
 
         5) Acute/Recent HIV Participants: Already on ART, without treatment interruption, either: 
 
a. Receiving co-formulated EFV 600 mg, FTC 200 mg, and TDF 300 mg; or 
  
b. Receiving co-formulated EVG 150 mg, COBI 150 mg, FTC 200 mg, and TDF 300 
mg (Stribild); or 
 
c. Receiving a combined ART regimen sponsored by the Peruvian MOH 
 
d. Prior/current participation in SABES and now receiving a non-EFV or EVG regimen 
with 3 active drugs (3 drugs not inclusive of the boosting agents COBI or ritonavir) 
 
 
6) Seronegative participants with acute HIV infection (lack of antibodies against HIV and 
presence of HIV-1 RNA. 
 
 
 
7) Kidney, liver, and hematologic functions should not prohibit ongoing administration of 
study drugs or else another clinically-appropriate 3-drug ART regimen (3 active drugs not 
inclusive of boosting agents ritonavir or COBI) 
 
 
   8) HIV Viral load <1000 copies/ml on the last available result (either routine clinical or study 
result). 
 
   9) No medical or psychiatric conditions that render the person a poor study participant in the 
opinion of the study physician. 
 
        10) Co-enrollment with other protocols will be at the investigators discretion. 
 
8.1.2 Exclusion Criteria 
 
1) Chronic hepatitis B co-infection   
 
2) Use of drugs that are highly dependent on CYP3A for clearance (such as rifampin) which 
preclude administration of one of the study ART regimens or else other clinically-indicated 
3-drug ART regimen 
 
3) Concurrent use of aminoglycosides, IV amphotericin B, cidofovir, cisplatin, foscarnet, IV 
pentamidine, probenecid, adefovir or immunomodulatory agents 
 

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4) Any other medical or social condition that in opinion of the Investigator could affect the 
assessment of study objectives or put volunteers at risk. 
 
 
 
8.2 RECRUITMENT 
 
After the completion of the last SABES Study visit, participants on ART will be invited to participate 
in the MERLIN Study.  Participants who have already completed follow-up in the SABES Study 
and were retained in clinical follow-up at IMPACTA and other clinics and received ART through a 
Peruvian MOH program will also be invited to participate.  SABES participants will be eligible to 
transfer to the MERLIN Study (either at the end of their 48-week follow-up or when the MERLIN 
Study opens whichever occurs later). 
 
To complete the initial cohort of the SABES 2017 study, enrollment will be offered to additional 
participants with acute HIV infection if those were diagnosed while seronegative, at the study site 
or collaboration institutions, and if they are interested in initiating antiretroviral treatment 
immediately in this study.  
 
9. STUDY TREATMENT 
 
9.1 TREATMENT REGIMENS 
All participants receiving EFV-based will receive EVG/COBI/FTC/TAF. 
 
EVG/COBI/FTC/TAF will be initiated in all participants because of the benefit of TAF compared 
with TDF and could have an improved metabolic risk and has demonstrable benefit on renal and 
bone protection 
 
All Group C participants should be transitioned to EVG/COBI/FTC/TAF as soon as drugbecomes 
available for distribution in the study.  
 
All participants in groups A and B who initiated EVG/COBI/FTC/TDF should transition to 
EVG/COBI/FTC/TAF as soon as that drug becomes available in the study.  
 
Participants who have initiated EVG/COBI/FTC/TAF could be switched to other antiretroviral    
treatment only if there is evidence of intolerance.  
 
 
 
 
 
 

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Figure 2.  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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9.2 ADMINISTRATION 
EVG/COBI/FTC/TAF or EVG/COBI/FTC/TDF will be administered as one tablet orally once daily 
with food. Other ART regimens will be administered as per respective packet instructions. 
 
9.3 DURATION 
Participants will remain in the study through 2022 (about 5 years), regardless of time since HIV 
diagnosis and/or completion of the Sabes protocol. The visit weeks for MERLIN will continue to 
be counted with respect to HIV diagnosis/Sabes 3 enrollment.  ART will be provided by the study 
for the duration of the time that the participant remains in the study.  At the end of study, 
participants will continue ART from other sources, including transition to Peruvian MOH clinics. 
 
9.4 STUDY PRODUCT FORMULATION AND PREPARATION 
Elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide (GENVOYA®) is co-formulated to 
contain 150 mg of elvitegravir, 150 mg of cobicistat, 200 mg of emtricitabine, and 10mg of 
tenofovir alafenamide in each tablet.   
 
Emtricitabine/tenofovir DF (Truvada®) is co-formulated to contain 200 mg of emtricitabine and 300 
mg of tenofovir DF and will be available when will be necessary to change the antiretroviral 
treatment.  
 
Each bottle of the described medicaments contain a silica gel desiccant that should be kept in its 
original recipient to protect the product from humidity.  The original recipient can be dispensed. 
Store at 25°C (77°F), variations from 15°-30°C (59°-86°F) are allowed.  
 
9.5 PRODUCT SUPPLY 
Co-formulated EVG/COBI/FTC/TDF (STRIBILD®) and EVG/COBI/FTC/TAF (GENVOYA®) will 
be provided by Gilead Sciences, Inc.  Co-formulated emtricitabine/tenofovir DF (Truvada®) will be 
provided by Gilead Sciences, Inc.  Truvada will be used only in combination with at  least a third 
antiretroviral. Per discretion of the  investigators, other drugs could  be provided procured locally 
if one of the listed study drugs cannot be used.  
 
9.6 PHARMACY FACILITIES 
The pharmacy facilities are located at the IMPACTA Barranco and IMPACTA San Miguel Clinical 
Research Sites and both are staffed by registered trained pharmacists.  Both pharmacies will 
have adequate space to store sufficient quantities of study agent to assure continuous access to 
all study participants.  The study drug will be stored in accordance with the drug manufacturer’s 
recommendations. Both pharmacies’ storage and the study pharmacies will be locked by a secure 
door. The pharmacies and storage facilities have climate-controlled environments, with controlled 
humidity and temperature to remain within limits allowed by the manufacturer for drug storage. 
 

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9.7 DRUG INVENTORY 
The pharmacists at the IMPACTA Barranco and IMPACTA San Miguel Clinical Research Sites 
will receive the study agent and store it in the pharmacy.  Access will be restricted to authorized 
pharmacy personnel only.  The pharmacists will be responsible for keeping accurate records of 
the material received.  At the end of the study, the pharmacists will perform the final drug 
accounting of unused study material on the proper log documents.  Unused study agent will be 
disposed of in accordance with local regulations.  
 
9.8 DRUG DISPENSING 
The Study Pharmacist will be responsible for dispensing the drug to the Study Nurse who will 
deliver it to the participant.  At each visit, the pharmacist will receive the prescription that includes 
the participant’s enrollment ID number.The pharmacist will dispense the drug according to the 
procedures shown in Figure 2. For bottle dispensed, the pharmacist will enter the packed label 
information and date in a Drug Dispensation Log, to be kept secure in the Pharmacy. 
 
9.9 CONCOMITANT MEDICATIONS 
To avoid adverse events caused by drug interactions, investigators must refer to the most recent 
package insert for study drug and concomitant agents whenever a concomitant medication is 
initiated or a dose is changed. 
 
Research sites must also refer to the study product’s most recent package insert or investigator 
brochure to access additional current information on prohibited and precautionary medications. 
 
Below are lists of selected concomitant medications.  These lists are only current as of the date 
of this protocol.  Therefore, whenever a concomitant medication or study agent is initiated or a 
dose changed, investigators must review the concomitant medication’s and study agent’s most 
recent package inserts or investigator brochure to obtain the most current information on drug 
interactions, contraindications, and precautions. 
 
9.9.1 Precautions with Concomitant Medications 
 
Package inserts of antiretroviral drugs and concomitant agents should be referenced whenever a 
concomitant medication is initiated or a dose is changed to avoid drug interaction AEs. 
 
9.9.2 Prohibited Medications  
 
Co-administration with drugs that are highly dependent on CYP3A for clearance and for which 
elevated plasma concentrations are associated with serious and/or life-threatening events is 
contraindicated. These drugs and other contraindicated drugs (which may lead to reduced 
efficacy of STRIBILD and possible resistance) are listed in the table below.  
 
 
 
 
 
 
 

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Table 1a: Drugs that are Contraindicated with STRIBILD and GENVOYA 
 MEDICATION CLASS  
PROHIBITED MEDICATIONS  
ALPHA 1-ADRENORECEPTOR ANTAGONIST  
Alfuzosin  
ANTIMYCOBACTERIAL  
Rifampin  
ERGOT DERIVATIVES  
Dihydroergotamine  
Ergotamine  
Methylergonovine  
GI MOTILITY AGENT  
Cisapride  
HERBAL PRODUCTS  
St. John’s wort (Hypericum perforatum)  
HMG-COA REDUCTASE INHIBITORS 
Lovastatin 
Simvastatin 
NEUROLEPTIC  
 
Pimozide  
 
PHOSPHODIESTERASE-5 (PDE5) INHIBITOR  
 
Sildenafil when dosed as REVATIO for the 
treatment of pulmonary arterial hypertension  
 
SEDATIVE/HYPNOTICS 
Triazolam 
Orally administered midazolam 
 
* Some brand names are showed, but attention must be taken about the generic name. 
** A single dose of midazolam may be used for sedation in subjects undergoing procedures in a 
monitored setting. 
 
 
9.9.3 Options for Medication Substitutions Due to Intolerance/Toxicity 
 
If intolerance or toxicity occurs, substitutions may be made to the study regimen, after discussion 
with the Protocol Chair, as long as the new regimen is consistent with current guidelines for potent 
ART.  The substituted medications will be provided by the study for the duration of time that the 
participant remains in the study.  The purpose of the study is to determine whether ART in general, 
not necessarily a specific regimen, affects the long-term clinical benefit for MSM and TG with 
different alcohol consumption levels, who acquired HIV recently. However, because in this study 
we are performing additional analysis comparing treatments based on EFV and EVG, those 
participants undergoing these medicament substitutions could be excluded from such secondary 
analyses.  
 
9.9.4 Options for Medication Substitutions for Virologic Failure 
 
If a subject develops virologic failure on the study regimen further management based in clinical 
judgment should proceed at the discretion of the On-Site Principal Investigator in consultation 
with the Protocol Chair or Co-Chair. 
 

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Substitutions in antiretroviral regimens during the course of the study are at the discretion of the 
site investigator. It is the site investigator's responsibility to review all concomitant medications to 
ensure safety. The protocol pharmacist is available for discussion if questions arise. 
 
The substituted medications will be provided by the study for the duration of time that the 
participant remains in the study. 
 
9.10 ADHERENCE ASSESSMENT 
Adherence will be assessed via validated self-report measures, pharmacy refill-based measures, 
and unexpected increases in HIV plasma viral load. Specifically, the Visual Analogue Scale [49] 
and the Ability Likert item [50] will be used to collect self-reported adherence over the past 30 
days, collected monthly. These measures have demonstrated consistent associations with viral 
load in other studies [51]. Because self-report has a number of limitations, including a tendency 
of over-estimate adherence in comparison to electronic drug monitoring measures as well as 
potentially high demands on other cognitive processes to produce accurate reports [52], we also 
will monitor pharmacy dispensation records to produce medication possession ratios (days 
covered by a prescription/days between scripts) in approximately 3-month intervals. Pharmacy-
based measures of adherence have consistently been associated with clinical outcomes in 
previous research [53, 54]. We will not monitor ART blood levels because 1) this is not done as 
part of routine clinical practice, 2) the tests would only refer to recent adherence rather than 
adherence over time, and 3) it is rather expensive to conduct these tests. 
 
10. STUDY PROCEDURES 
 
10.1 Visit Program 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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Procedures 
and 
Sample collection 
Reference 
to Arm of 
ART 
initiation in 
SABES 3 
ENR 
(Enrollment 
with 
acute 
infection 
diagnosis) 
Study 
week 
+/- 28 days 
ENR 
3, 4 
(enrollme
nt 
after 
SABES 
participati
on) 
Study week 
(counted since enrollment into SABES study –after HIV diagnosis) 
+/- 8 weeks of window 
12 
24 
36 
48 
72 
96 
120 
144 
168 
192 
216 
Annual Visits 
Bi-annual 
visits 
Every 
48 
weeks 
after 
wk 
192 for the 
immediate 
arm 
 (I) 
Every 
48 
weeks 
after 
wk 
216 for the 
deferred 
arm 
 (D) 
Every 
24 
weeks after: 
Wk 192 = I   
Wk216 = D 
Informed Consent 
both 
X 
 
 
 
 
X 
 
 
 
 
 
 
 
 
 
 
Clinical Procedures5 
both 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Questionnaire (CASI) 
both 
X 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Pneurophsycologic 
test 
both 
X 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
Abdominal 
circunference* 
both 
 
 
 
 
 
X 
√ 
√ 
√ 
X 
 
 
X 
X 
X 
 
Stool 
New ENR  
Immediate 
X 
 
X 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
 
 
 
Collection 
in the past 
both 
 
 
 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
No 
collection 
in the past 
Immediate 
 
 
 
 
 
 
 
 
 
 
 
X1 
 
 
 
 
Deferred 
 
 
 
 
 
 
X1 
 
 
 
Rectal biopsy 
and 
secretion  (N=60) 
Immediate 
 
 
 
 
 
 
 
X 
 
X 
 
X 
 
 
 
 
Deferred 
 
 
 
 
 
 
 
 
X 
 
X 
 
X 
 
 
 
Urine  
Both 
X 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 

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BLOOD 
ART 
safety 
tests 
(Biochemistry, 
liver 
function 
and 
hematology)  
both 
X 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
CD4/CD8 
both 
X 
 
 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
HIV viral load 
both 
X 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Lipid panel** 
both 
X 
 
 
 
X 
X2 
√2 
√2 
√2 
X 
 
 
X 
X 
X 
 
Glucose** 
both 
X 
 
X 
 
X 
X2 
√2 
√2 
√2 
X 
 
 
X 
X 
X 
 
PBMC 
both 
X 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
Plasma 
both 
X 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
Whole blood (RNA 
LATER) 
both 
 
 
 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 

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Procedures 
and 
sample collection 
Reference 
to Arm of 
ART 
initiation in 
SABES 3 
ENR 
(Enrollment 
with 
acute 
infection 
diagnosis) 
Study 
week 
+/- 28 days 
ENR 
3, 4 
(enrollme
nt 
after 
SABES 
participati
on) 
Study week 
(counted since enrollment into SABES study –after HIV diagnosis) 
+/- 8 weeks of window 
12 
24 
36 
48 
72 
96 
120 
144 
168 
192 
216 
Annual Visits 
Bi-annual 
visits 
Every 
48 
weeks 
after 
wk 
192 for the 
immediate 
arm 
 (I) 
Every 
48 
weeks 
after 
wk 
216 for the 
deferred 
arm 
 (D) 
Every 
24 
weeks after: 
Wk 192 = I   
Wk216 = D 
Leukapheresis 
(N=40) 
Inmediato 
 
 
 
 
 
 
 
X 
 
X 
 
X 
 
X 
 
 
Diferido 
 
 
 
 
 
 
X 
 
X 
 
X 
 
X 
 
X 
 
Dried  blood 
ambos 
 
 
 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
Syphilis tests 
ambos 
 
 
 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
Max 
volumen 
of 
blood (ml)  
Including 
leukapheresis 
(if 
applicable) 
ambos 
250 
 
250 
 
250 
250 
250 
250 
250 
250 
250 
250 
250 
250 
250 
30 

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√ conditiona procedure  
X obligatory procedure 
 
* The measurement must be taken the same day of simple collection for lipid panel and glucose 
 
** fasting 
 
 
 
1 for those in which stool sample was not collected in the Sabes 3 enrollment visit, the sample must be    taken 
in week 192 for the immediate arm participants and in week 216 for the deferred arm participants.   
  
 2 the sample for lipid panel and glucose must be taken during fasting; however, if the participant is not fasting 
during the enrollment visit, the simple can be recovered in the immediately following visit.   
 
 3 If the enrollment visit occurs within 8 weeks after the Observational study “Collaborative Studies of the Effect 
of Very Early Initiation of ART and Development of HIV Incidence Assays in Lima, Peru”) visit, it will not be 
necessary to collect samples collected during such visit (PBMC, stool, urine); the only sample to be collected 
will be for safety test, CD4/CD8, viral load, lipid panel and glucose. 
 
 4 If the enrollment visit occurs within the window period of the week visits, 72, 96, 120, 144, 168, 192, 216 or 
the following every 6 month visits; then it will not be necessary to collect samples already obtained in the 
enrollment visit (PBMC, stool, urine) in the next follow-up visit;  only  a sample to run safety tests should be 
collected.  
 
5 Medical chart evaluation, physical exam, concomitant medication and diagnosis will be performed.  
 
6 For participants in the Group D and any other who did not have lumbar puncture before 2018,  the lumbar 
puncture procedure will not be done in weeks 96/120, but only after week 144 (based on  study arm).  
 
7 The last lumbar puncture procedure will be done at week 240 for the immediate arm and week 264 for the 
deferred arm.  
 
 
10.2 RECRUITMENT 
 
10.2.1 SABES 3 Participants 
 
SABES 3 Participants will be recruited from current SABES study participants at any time during 
SABES 3 follow-up, immediately after the week 48 visit, or after they have entered follow-up care 
at IMPACTA or TARGA Clinical sites.   
. 
10.2.2 New participants with acute infection 
 
Up to 25 new participants with acute hiv infection will be enrolled. The diagnosis will be done 
during the acute phase of HIV infection (positive HIV RNA test  or p24 antigen with negative HIV 
antibody test) at the IMPACTA site or other collaboration institutions.  These participants will 
rapidly be referred to this study.  
 
 
10.3 TIMING OF VISITS 
10.3.1 Enrollment Assessments 
 
10.3.1.1 Participants from SABES step 3 

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The enrollment into the MERLIN study can occur at any time after having completed SABES Step 
3, including immediately after the final visit of SABES. 
 
10.3.1.2 New participants with acute HIV diagnosis 
 
The new participants entering with acute HIV diagnosis will be enrolled as soon as possible after 
HIV diagnosis.  
 
10.3.2. Follow-up Assessments 
 
10.3.2.1 Participants from SABES step 3 
 
The MERLIN study visits should occur at 24-week intervals with respect to SABES enrollment, 
rather than with respect to MERLIN enrollment in order to preserve time-points with respect to 
date of SABES enrollment and ART randomization  
 
If the participant received MOH-based ART after completing SABES, the study visit schedule 
should resume a 24-weekly schedule with respect to timing from SABES enrollment, at the next 
possible visit (e.g. 72, 96, 120, etc., weeks). 
 
10.3.2.2. New participants with acute HIV diagnosis 
 
Participants who enroll into MERLIN immediately after acute HIV diagnosis will initiate ART 
treatment within 72 hours after the enrollment visit and will have follow-up visits following Peruvian 
clinical care guidelines.  
 
10.3.3 Last study visit 
 
The planned last study visit is not a particular numerical week, but rather will occur on or before 
December 31, 2022.  All participants may remain involved in MERLIN for approximately 5 years, 
regardless of interval between the two studies. 
 
 
10.3.4  Definitions of evaluations and special indications 
10.3.4.1 Medical History 
 
A medical history must be present in source documents.  The medical history should be 
comprehensive and include HIV-1 related and non-related diagnoses.  The medical history from 
SABES Step 3 should be reviewed and updated if appropriate. HIV uninfected and chronic HIV 
infection participants should have a medical history collected. 
 
10.3.4.2 Medication History 
 
A medication history must be present in source documents, including any history of antiretroviral 
medication, immune-based therapy, or HIV-1-related vaccines, including blinded study 
medications. 
 

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All prescription medications taken within 30 days prior to study entry, including actual or estimated 
start and stop dates, should be included in both the source documents and on the case report 
forms (CRFs). 
 
All nonprescription medications taken within 30 days prior to study entry, including actual or 
estimated start and stop dates, should also be included in source documents. 
 
10.3.4.3 Concomitant Medications 
 
All of the concomitant medications taken since the last report should be registered in the source 
documents and the CRF and should include the start and end dates. 
 
10.3.4.4 Modifications of Study Treatment Regimen 
 
All of the pharmacologic modifications including the initial doses begun by the subject and/or 
interruptions proscribed by the protocol, modifications, and permanent suspension of the 
treatment should be recorded at ever visit in the source documents and the CRF 
 
10.3.4.5 Clinical Assessments 
 
1. Complete physical exam 
A complete physical exam is to be performed at study entry and study completion. 
 
2. Targeted physical exam 
A targeted physical examination is required as clinically indicated. 
 
3. Height to be collected at study entry. 
 
4. Weight to be collected at all study visits.  
 
5. Vital signs 
Oral temperature, pulse, and blood pressure to be collected at all visits. 
 
6. Waist circumference should be measured at the enrollment (or the following visit ) when 
the sample for lipid panel and glucose (fasting) is taken, as well as during week 144 and 
216.  
 
7. Signs and symptoms 
All signs, symptoms, and toxicities at entry must be documented in the subject’s record 
and on the CRFs.  Unless otherwise specified, after entry, only grade ≥ 3 and all signs 
and symptoms that led to a change in treatment, regardless of grade, must be recorded 
on the CRFs.  The “Division of AIDS Table for Grading the Severity of Adult and Pediatric 
Adverse Events Version 1.0, December, 2004; Clarification August 2009” must be used 
and is available at http://rsc.tech-res.com/safetyandpharmacovigilance. 
 
8. Diagnoses 
All confirmed and probable diagnoses made since the last visit must be recorded in the 
source documents and CRFs.  The following diagnoses will be recorded in source 

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documentation and CRFs: U.S. Center for Disease Control and Prevention Category B 
and C diagnoses, major organ disease including but not limited to diabetes, cardiovascular 
disease and stroke, hepatitis, avascular necrosis, fat redistribution including central fat 
accumulation and peripheral fat wasting (as noted by subject and site staff and/or primary 
care provider). Please refer to AIDS Clinical Trials Group Appendix 60 for specific 
diagnoses 
and 
definitions 
which 
can 
be 
found 
at 
http://www.hptn.org/web%20documents/HPTN052/Appendix60V1.123Feb2007.pdf. 
 
9. Neuropsychiatric Testing 
As part of the assessment of neuroinflammation in acute/recent HIV, each participant will 
undergo neuropsychiatric testing during each study visit. The visit will follow Study specific 
procedure (SSP) for neuropsychiatric testing. 
 
10.3.4.6 Questionnaires 
 
Questionnaires will be self-administered by participants at each visit (every 24 weeks). The 
questionnaire will take approximately 60 minutes in each visit.   
 
This questionnaire will contain several modules:  
 
1. Drug and alcohol use [drug use history, DAST 10 (drug abuse screening test) , drinking 
expectancies];  
2. Mental health and well-being [RAND 12 (health well-beign) , Social support scale, Stigma 
scale, Stigma and diagnoses disclosure, Partner notification, Intimate partner violence, 10 
item CES-D (depression scale), Mental health items on anxiety,  Stress & Coping];  
3. Medical care (hospitalization and ER use, Barriers to care, Access to care, Self-efficacy 
for ART use).  
 
10.3.4.7 Laboratory Assessments 
 
The “Division of AIDS Table for Grading the Severity of Adult and Pediatric Adverse Events 
Version 1.0, December, 2004; Clarification August 2009” must be used and is available at 
http://rsc.tech-res.com/safetyandpharmacovigilance. 
 
All baseline laboratory values must be documented in the subject’s record and recorded on the 
CRFs.  Subsequently, all laboratory values must be documented in the subject’s record, but 
unless otherwise specified, only laboratory values Grade ≥ 3 must be recorded on the CRFs.  Any 
laboratory toxicity that led to a change in treatment, regardless of grade, must be recorded on the 
CRFs.  Laboratory evaluations that do not have a grading scale in the “Division of AIDS Table for 
Grading the Severity of Adult and Pediatric Adverse Events Version 1.0, December, 2004; 
Clarification August 2009” must be collected on the CRFs if the values are outside the upper or 
lower limit of normal 
 
1. Hematology 
Hemoglobin, white blood cell count, absolute neutrophil count, platelets; 
 
2. Blood chemistries  
Serum amylase, lipase, bicarbonate, phosphorus, creatinine, AST (SGOT), ALT (SGPT), 

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alkaline phosphatase. 
 
3. Lipid panel and glucose 
Subjects should be fasting for at least 8 hours for blood sample collection for lipid panel 
and glucose measurements.  These tests will be performed in the enrollment visit and 
follow-up visits week 144 and 216. If the participant is not fasting, the tests must be 
deferred and will be taken during the next programmed visit.  
 
Triglycerides, total cholesterol, HDL, LDL and glucose.  
 
4. Urinalysis 
Dipstick, and microscopic exam if dipstick is positive;   
Additionally urine samples will be stored for future drug analyses and STD tests.  
 
 
5. Sexually transmitted infection testing 
Syphilis screening testing will be conducted by RPR and confirmed by MHA-TP if reactive.  
Syphilis diagnosis will follow Ministry of Health of Peru guidelines.  A positive leukocyte 
esterase test by a urine dipstick will trigger a microscopic examination.   
 
Samples will be stored for further confirmation with a nucleic acid amplification test for N. 
gonorrhoeae and C. trachomatis if a diagnosis of urethritis is made. The results of these 
tests will be for research purposes only.  
 
Participants with a positive leukocyte esterase test and/or with symptoms will receive 
treatment following the local standard of treatment.   
 
10.3.4.8 Immunologic Studies 
 
1. CD4+/CD8+ T-cell subsets 
A CD4+ T-lymphocyte percent of total lymphocytes and CD8+ T-lymphocyte percent of 
total lymphocytes should be performed in addition to the absolute CD4+ and CD8+ T cell 
counts at screening and for all visits at which CD4+/CD8+ T cell counts are required.  
Because of the diurnal variation in CD4+ and CD8+ cell counts, determinations for 
individual subjects should be obtained consistently in either the morning or the afternoon 
throughout the study, if possible. 
 
NOTE: Each time a CD4+/CD8+ measurement is obtained, the local laboratory must 
perform a WBC and differential from a sample obtained at the same time. 
 
10.3.4.9 Virologic Studies 
 
1. Plasma HIV-1 RNA 
All HIV-1 RNA testing will be performed using the Abbott m2000 RealTime System (Abbott 
Molecular) at the IMPACTA PERU Clinical Trials Unit Central Laboratory, which is certified 
by the U.S. NIH/NIAID/DAIDS Virology Quality Assurance (VQA) Program. The baseline 
value will be the HIV-1 RNA level at the entry evaluation. 
 

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The results from the analysis of Plasma HIV-1 RNA at each 24-weekly visit will be 
available at the next follow-up visit to guide the medical management decision-making for 
each participant, according to the HIV management standards.  Samples for HIV-RNA 
taken more frequently (from SABES timepoints) will not be used clinically and will only be 
used for research purposes and therefore will not be processed in real time. 
 
2. HIV-1 genotype in stored samples will be performed by the University of Washington 
Virology Specialty Laboratory/Seattle Children’s Hospital at the end of the study or when 
required per clinical judgment at time of suboptimal virologic response. 
 
10.3.4.10 Leukapheresis  
 
A subset of MERLIN participants (N = 40) will undergo leukapheresis.  There is a separate 
consent form and only those who are newly enrolled and volunteer for this procedure will have it 
performed.  Qualitative and quantitative assessment of the HIV reservoir (including its localization 
in different CD4+ T cell subsets) will require large numbers of cells, which is important as both 
size and distribution of the HIV reservoir will be key factors in strategies to induce a functional 
cure. Thus, we will use leukapheresis to collect large samples at critical time points (SABES 
baseline and 24 weeks on all participants, then 72, 120, and 216 weeks for deferred  arm, and 
96, 144, and 196 weeks for immediate Arm). 
 
10.3.4.11 Stored Plasma, PBMC, Whole Blood in RNA later 
 
At all time points, whole blood, plasma, and PBMC will be stored for later analysis, many of which 
are described in the analysis plan, or else are for future studies as per specimen repository 
consents. 
 
10.3.4.12 Stool Samples 
 
Stool will be collected (25g per visit) at the visits indicated in the procedures table, for the  
evaluation of the microbiome throughout phases of VIH infection (acute-recent- and treated HIV 
infection) In one of the collaborative studies associated to this study, stool samples were 
collected.  If these participants are enrolled in MERLIN they will be asked to provide stool samples 
in all the visits; however, for those participants who were not enrolled in the collaborative study 
and for who stool sample was not collected previously, only one sample will be requested during 
week 168 for the participants in the immediate SABES 3 arm, and during week 192 for those 
enrolled in the deferred SABES 3 arm.  
 
10.3.4.13 Rectal Biopsies and Rectal Secretions 
 
Rectal biopsies will be performed in a subset of 60 participants who additionally consent, using a 
separate informed consent procedure, to up to 4-3 rectal biopsies. Rectal secretions will be 
collected via a swab or sponge at the time of biopsy.  In Immediate arm participants, the biopsies 
will be performed at 96, 144 and 192; ; in the Deferred arm, biopsies will occur at 120, 168 and 
216 weeks.  Biopsy procedure will be performed  following  the SSP. 
 
10.3.4.14 Lumbar Puncture (LP) 

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A subset of up to 40 participants, ideally evenly dispersed between Immediate and Deferred Arms 
will undergo lumbar puncture to obtain cerebrospinal fluid (CSF).  Those approached for CSF 
evaluation will sign a separate informed consent for this procedure and no MERLIN participants 
will undergo LP without signing a consent.  LP will be performed in the specified visits as indicated 
in the table of procedures.  Refer to the SSP for LP procedures. 
 
 
11.WARNINGS AND PRECAUTIONS  
 
11.1 LACTIC ACIDOSIS/SEVERE HEPATOMEGALY WITH STEATOSIS 
 
Lactic acidosis and severe hepatomegaly with steatosis, including fatal cases, have been reported 
with the use of nucleoside analogs alone or in combination with other antiretrovirals.  A majority 
of these cases have been in women.  Obesity and prolonged nucleoside exposure may be risk 
factors.  Particular caution should be exercised when administering nucleoside analogs to any 
patient with known risk factors for liver disease; however, cases have also been reported in 
patients with no known risk factors. 
 
Treatment with co-formulated EVG/COBI/FTC/TAF should be suspended in any patient who 
develops clinical or laboratory findings suggestive of lactic acidosis or pronounced hepatotoxicity 
(which may include hepatomegaly and steatosis even in the absence of marked transaminase 
elevations). 
 
11.2 PATIENTS WITH HIV AND HBV COINFECTION 
It is recommended that all patients with HIV be tested for the presence of hepatitis B before 
initiating antiretroviral therapy.  Co-formulated EVG/COBI/FTC/TDF or EVG/COBI/FTC/TAF is not 
indicated for the treatment of chronic HBV infection and the safety and efficacy of these co-
formulated regimenshave not been established in patients co-infected with hepatitis B virus and 
HIV.  Severe acute exacerbations of hepatitis B have been reported in patients after the 
discontinuation of emtricitabine and tenofovir DF.  Hepatic function should be closely monitored 
with both clinical and laboratory follow-up for at least several months in patients who discontinue 
co-formulated EVG/COBI/FTC/TDF or EVG/COBI/FTC/TAF and are co-infected with HIV and 
HBV. 
 
HIV-1/hepatitis B co-infected individuals will not be enrolled in this study.   
 
11.3 NEW ONSET OR WORSENING RENAL IMPAIRMENT  
Renal impairment, including cases of acute renal failure and Fanconi syndrome (renal tubular 
injury with severe hypophosphatemia), has been reported with the use of tenofovir DF, and 
its co-formulations.  Estimated creatinine clearance, urine glucose and urine protein should 
be documented in all patients prior to initiating therapy. Initiation of co-formulated 
EVG/COBI/FTC/TDFin patients with estimated creatinine clearance below 70 mL per minute 
is not recommended. Initiation of EVG/COBI/FTC/TAF in patients with estimate creatinine 
clearance <30 ml/min is not recommended. 
 

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Co-formulated EVG/COBI/FTC/TDF and co-formulated EVG/COBI/FTC/TAF should be avoided 
with concurrent or recent use of a nephrotoxic agent (e.g., high-dose or multiple non-steroidal 
anti-inflammatory drugs (NSAIDs)). Cases of acute renal failure after initiation of high dose 
or multiple NSAIDs have been reported in HIV-infected patients with risk factors for renal 
dysfunction who appeared stable on tenofovir DF. Some patients required hospitalization and 
renal replacement therapy. Alternatives to NSAIDs should be considered, if needed, in 
patients at risk for renal dysfunction. Persistent or worsening bone pain, pain in extremities, 
fractures and/or muscular pain or weakness may be manifestations of proximal renal 
tubulopathy and should prompt an evaluation of renal function in at-risk patients.  
 
Routine monitoring of estimated creatinine clearance, urine glucose, and urine protein should 
be performed during co-formulated EVG/COBI/FTC/TDF or EVG/COBI/FTC/TAF therapy in all 
patients. Additionally, serum phosphorus should be measured in patients at risk for renal 
impairment.  
 
Although COBI may cause modest increases in serum creatinine and modest declines in 
estimated creatinine clearance without affecting renal glomerular function, patients who 
experience a confirmed increase in serum creatinine of greater than 0.4 mg per dL from 
baseline should be closely monitored for renal safety.  
The FTC, TAF, and TDF are primarily excreted by the kidney. Co-formulated 
EVG/COBI/FTC/TDF should be discontinued if estimated creatinine clearance declines below 
50 mL per minute as dose interval adjustment required for emtricitabine and tenofovir DF 
cannot 
be 
achieved 
with 
the 
fixed-dose 
combination 
tablet. 
Co-formulated 
EVG/COBI/FTC/TAF should be discontinued if the creatinine clearance falls below 30 mL/min. 
 
11.4 LIVER ENZYMES 
In patients with known or suspected history of hepatitis B or C infection and in patients treated 
with other medications associated with liver toxicity, monitoring of liver enzymes is recommended. 
In patients with persistent elevations of serum transaminases to greater than five times the upper 
limit of the normal range, the benefit of continued therapy with co-formulated study treatment 
needs to be weighed against the unknown risks of significant liver toxicity. 
 
Because of the extensive cytochrome P450 mediated metabolism of efavirenz and limited clinical 
experience in patients with hepatic impairment, caution should be exercised in administering co-
formulated study treatments to these patients. 
 
11.5 FAT REDISTRIBUTION 
Redistribution/accumulation of body fat including central obesity, dorsocervical fat enlargement 
(buffalo hump), peripheral wasting, facial wasting, breast enlargement, and "cushingoid 
appearance" have been observed in patients receiving antiretroviral therapy. The mechanism and 
long-term consequences of these events are currently unknown. A causal relationship has not 
been established. 
 
11.6 IMMUNE RECONSTITUTION SYNDROME 
Immune reconstitution syndrome has been reported in patients treated with combination 
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combination antiretroviral treatment, patients whose immune system responds may develop an 
inflammatory response to indolent or residual opportunistic infections (such as Mycobacterium 
avium infection, cytomegalovirus, Pneumocystis jiroveci pneumonia (PCP), or tuberculosis), 
which may necessitate further evaluation and treatment. 
 
Autoimmune disorders (such as Graves’ disease, polymyositis, and Guillain-Barré syndrome) 
have also been reported to occur in the setting of immune reconstitution, however, the time to 
onset is more variable, and can occur many months after initiation of treatment. 
 
11.7 CO-ADMINISTRATION WITH RELATED DRUGS 
Co-formulated EVG/COBI/FTC/TAF is indicated for use as complete regimens for the treatment 
of HIV-1 infection and co-administration with other antiretroviral products is not recommended.  
Co-formulated EVG/COBI/FTC/TAF is not recommended for coadministration with the 
following:  
• 
Product containing emtricitabine or tenofovir DF (ATRIPLA, COMPLERA, EMTRIVA, 
TRUVADA, VIREAD)  
• 
Products containing lamivudine (COMBIVIR, EPIVIR, EPIVIR-HBV, EPZICOM, 
TRIZIVIR) or adefovir dipivoxil (HEPSERA) 
• 
ritonavir (NORVIR, KALETRA) 
 
12. MANAGEMENT OF TOXICITIES 
12.1 CLINICAL TOXICITIES 
Clinical AEs will be evaluated by the study physicians.  Grade 3 and 4 clinical AEs will be referred 
to On-Site Principal Investigator at the time of the visit.  A back-up coverage schedule will be 
developed and posted to assure that a study physician is available to the On-Site Principal 
Investigator responsible for medical decision-making, by phone at all times. 
 
12.1.1 Nausea and Vomiting 
 
12.1.1.1 Grade 1 or 2 
Study treatment should continue without interruption. Subjects with Grade 1 and 2 nausea or 
vomiting may be treated symptomatically with permitted oral antiemetic therapies or antiemetic 
suppositories provided there is no suspicion of lactic acidosis or pancreatitis. 
 
12.1.1.2 Grade ≥ 3  
Subjects with Grade ≥ 3 nausea and vomiting should interrupt all study treatment until the toxicity 
grade returns to Grade 2 or to baseline.  However, substitutions to the treatment regimen, as 
opposed to interruption of the entire regimen, may be made at the investigator’s discretion upon 
consultation with the Study Chair. If the nausea does not improve with the substitution, then all 
study treatment should be interrupted.  Once the toxicity returns to Grade 2 or baseline, study 
medications may be resumed. If Grade ≥ 3 nausea and vomiting recurs upon the resumption of 
study treatment, treatment should again be interrupted and alternative ART should be considered 
and discussed with the Study Chair.  If Grade ≥ 3 nausea or vomiting persists for more than 4 
weeks, then study treatment should be permanently discontinued. 
 
12.1.2 Diarrhea 
 

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12.1.2.1 Grade 1 or 2 
All subjects with study drug-related diarrhea should initially be treated symptomatically with 
antidiarrheal medications such as loperamide, diphenoxylate, and/or an aluminum hydroxide 
antacid.  Study drug administration may continue at the discretion of the investigator. 
 
12.1.2.2 Grade ≥ 3 Diarrhea 
Grade ≥ 3 diarrhea that is unresponsive to antimotility agents should prompt interruption of all 
study treatment until resolution of diarrhea to Grade ≤ 2 or baseline.  However, substitutions to 
the treatment regimen, as opposed to interruption of the entire regimen, may be made at the 
investigator’s discretion upon consultation with the Study Chair.  If the diarrhea does not improve 
with the substitution, then all study treatment should be interrupted.  Once the toxicity returns to 
Grade 2 or baseline, study medications may be resumed.  If Grade > 3 diarrhea recurs upon the 
resumption of study treatment, all study treatment should be interrupted and alternative ART 
should be considered and discussed with the Protocol Chair.  If Grade ≥ 3 diarrhea persists for 
more than 4 weeks, then study treatment should be permanently discontinued. 
 
12.1.3 Symptomatic Hyperlactatemia 
 
Occurrence of lactic acidosis is expected to be very rare with the medication regimen used in this 
protocol.  However, if an investigator suspects – due to symptoms or lab abnormality – lactic 
acidosis or symptomatic hyperlactatemia, a lactate level should be drawn. 
 
Symptomatic hyperlactatemia will be defined as new, otherwise unexplained and persistent 
occurrence for >2 weeks of one or more of the following in addition to an elevated lactate level: 
 
• 
nausea and vomiting 
• 
abdominal pain or gastric discomfort 
• 
abdominal distention 
• 
increased LFTs 
• 
unexplained fatigue 
• 
dyspnea 
• 
motor weakness 
 
If the lactate value is > 2 x ULN, obtain a confirmatory lactate value as soon as possible, preferably 
within 1 week.  Study treatment should be discontinued immediately if the confirmatory value 
remains > 2 x ULN or if the site is unable to obtain a confirmatory value within 1 week.  Determine 
lactate levels every 4 weeks until the lactate value returns to normal, at which time a new 
antiretroviral regimen may be constructed in consultation with the protocol team.  
 
Management of symptomatic lactate value < 2 x ULN will proceed at the discretion of the local 
investigator.  However, any modification of a subject's antiretroviral regimen should be made in 
consultation with the protocol team.   
 
12.2 LABORATORY TOXICITIES 
Laboratory results will be flagged by the laboratory as abnormal or critical using pre-determined 
criteria at the laboratory.  Abnormal values will be confirmed by repeat testing of the same 
specimen.  All critical values will be reported to On-Site Principal Investigator by cell phone or e-

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mail.  All results will be documented in laboratory records.  All laboratory test results will be 
reported.   
 
Participants who are not present at the study site at the time a critical value is identified will be 
contacted by telephone or in person and asked to come back to the study site for further 
evaluation, referral, and counseling.  
 
Grade 3 and 4 laboratory abnormalities should be confirmed by repeat testing preferably within 3 
calendar days of receipt of results and before study drug discontinuation, unless such a delay is 
not consistent with good medical practice.  All laboratory abnormalities that would lead to a 
change in treatment should be confirmed as soon as possible. 
 
12.2.1 Increases in Values for Liver Function Tests 
 
12.2.1.1 Asymptomatic 
For asymptomatic Grade 3 elevations of total bilirubin, AST, ALT, or alkaline phosphatase, study 
treatment may be continued at the discretion of the site investigator in consultation with the Study 
Chair.  Alternatively, the investigator may make substitutions to the antiretroviral regimen upon 
consultation with the Study Chair. 
 
If asymptomatic abnormalities in liver enzymes of Grade 3 persist for more than 4 weeks, the site 
investigator should consider temporary interruption of study treatment in consultation with the 
Protocol Chair. 
 
12.2.1.2 Symptomatic or Grade 4 
For symptomatic Grade 3 elevations of total bilirubin, AST, ALT, or alkaline phosphatase or for 
Grade > 3 elevations in AST, ALT, or alkaline phosphatase, all study treatment should be 
interrupted until the toxicity returns to Grade ≤ 2 or baseline, after which time all study treatment 
may be resumed. 
 
If asymptomatic liver enzyme elevations Grade > 3 or symptomatic liver enzyme elevations persist 
for more than 4 weeks, despite the interruption of all study treatment, or if liver function 
abnormalities recur to Grade ≥ 3 at any time after the resumption of study treatment, then all study 
treatment should be interrupted or discontinued and the Study Chair should be contacted 
regarding the reintroduction of study treatment or the selection of alternate ART. 
 
12.2.2 Lipase 
 
12.2.2.1 Grade ≥ 2 Asymptomatic 
If a Grade ≥ 2 elevation of lipase occurs, the subject should be evaluated for signs and symptoms 
of pancreatitis and additional diagnostic evaluation should be performed as clinically indicated. 
For asymptomatic Grade 2 or 3 elevations of lipase, study treatment may be continued at the 
discretion of the site investigator in consultation with the Protocol Chair.  Alternatively, the 
investigator may choose to substitute another antiretroviral agent for any of the components of 
the original study regimen. If Grade > 3 toxicity persists for more than 14 days despite interruption 
or substitution of study treatment, or recurs after reintroduction of study treatment, all study 
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selected at the discretion of the local investigator when appropriate resolution of pancreatitis 
occurs. 
 
Subjects with Grade 4 elevations in serum lipase without clinical symptoms of pancreatitis should 
have all study treatment interrupted until the toxicity returns to Grade < 1, then all study treatment 
or a substituted regimen may be restarted at full dose. 
 
12.2.2.2 Symptomatic Pancreatitis (Regardless of Lipase Grade) 
A diagnosis of pancreatitis should be considered if clinical symptoms such as nausea, vomiting, 
or abdominal pain are present.  Subjects with these signs and symptoms should be evaluated for 
the presence of pancreatitis through the use of diagnostic testing, which should include serum 
amylase, lipase, and triglyceride measurements and may include pancreatic imaging via 
abdominal ultrasound and/or CT scanning as clinically warranted.  If a diagnosis of pancreatitis is 
confirmed, all study treatment should be interrupted immediately. 
 
12.2.3 Triglycerides/Cholesterol 
Subjects with asymptomatic triglyceride elevations Grade > 3 may continue to receive study 
treatment at the discretion of the local investigator. In consultation with the Protocol Chair, the 
On-Site Principal Investigator may consider the addition of permitted lipid-lowering agents if 
necessary to treat hyperlipidemia. Dose interruptions or discontinuations of study treatment 
should be considered only for confirmed increased fasting triglycerides ≥ 1200 mg/dL. 
 
Elevations in triglycerides ≥ 1200 mg/dL: For participants with this level of  triglycerides,  a fasting 
triglycerides level test will need to be performed and also a serum amylase and lipase. . For Grade 
≥ 2 asymptomatic elevations in serum amylase and/or lipase (collected in response to elevated 
triglycerides) in the setting of Grade > 3 hypertriglyceridemia, subjects should be started on a 
fibrate, and amylase and lipase should be monitored every 2 weeks until amylase and lipase are 
Grade < 2. If symptoms of pancreatitis develop, study treatment should be interrupted until 
pancreatitis resolves, amylase, and lipase are Grade < 2 and hypertriglyceridemia is Grade < 3. 
Consideration should be given to continuing a fibrate if study treatment is reintroduced. 
 
Subjects may continue on all study treatment despite Grade ≥ 3 triglyceride elevations if they 
remain asymptomatic with close clinical follow-up. In consultation with the Study Chair, the 
concomitant administration of gemfibrozil, clofibrate, or fenofibrate may be considered. 
 
If Grade 4 triglyceride toxicity persists 4 weeks after the addition of medical intervention (addition 
of lipid-lowering agent), all study treatment should be interrupted. If Grade 4 toxicity persists for 
more than 14 days after all study treatment has been interrupted, consider permanent 
discontinuation of all study treatment and a new potent antiretroviral regimen should be selected 
at the discretion of the local investigator in consultation with the Study Chair. 
 
12.2.4 Hyperglycemia 
Appropriate dietary modifications and glucose-lowering agents should be initiated for subjects 
with hyperglycemia, at the discretion of the local investigator and in accordance with customary 
medical care. 
 

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12.2.5 Renal Insufficiency 
Tenofovir DF substitution should occur for a confirmed creatinine clearance < 50 ml/min until an 
underlying etiology is determined.  If no other etiology is determined or the renal insufficiency 
improves with holding tenofovir DF, tenofovir DF should be permanently discontinued. 
 
Baseline serum creatinine will be the mean of the screening and entry values.  If at any time 
serum creatinine is increased >1.5-fold above baseline, the serum creatinine should be repeated 
as soon as possible (preferably within one week).  Participants with confirmed serum creatinine 
increases >1.5-fold above baseline should undergo an evaluation for potential causes of 
decreased renal function.  Participants with confirmed increase in serum creatinine >1.5-fold 
above baseline should have serum creatinine monitored more frequently, at the discretion of the 
site investigator, until serum creatinine either stabilizes or decreases to ≤1.5-fold above baseline. 
Drug dosing adjustments should be done based on the calculated creatinine clearance. 
 
12.2.6 Hypophosphatemia 
For Grade 1 and Grade 2 hypophosphatemia, phosphorus should be repeated as soon as 
possible (within 2 weeks is optimal), and tenofovir DF may be continued without other signs of 
renal tubular acidosis at the discretion of the site investigator. 
 
For asymptomatic Grade 3 decreases in phosphorus, subjects may either substitute another 
nucleoside reverse transcriptase inhibitor (NRTI) for tenofovir DF, or may remain on tenofovir DF 
with the following caveats.  Subjects should be treated with oral phosphate supplements and 
phosphorus levels should be re-tested weekly until phosphorus returns to Grade 2 or better.  If 
Grade 3 or worse phosphorus levels persist, tenofovir DF should be discontinued and another 
NRTI should be substituted.  If Grade 4 hypophosphatemia occurs, tenofovir DF should be 
changed to an alternative NRTI in consultation with the Protocol Chair, and serum phosphorus 
levels should be followed weekly until resolution to Grade 2 or better. 
 
12.3 ALL OTHER GRADE 3 OR 4 TOXICITY 
Subjects who develop a Grade 3 adverse event or toxicity reasonably causally related to the study 
medications (with the exception of asymptomatic laboratory abnormalities) should have all their 
antiretroviral study medication held and the subject rechecked each week until the adverse event 
returns to Grade < 2. If the investigator has compelling evidence that the adverse event has not 
been caused by the study medication or has another acceptable management plan, dosing may 
continue after discussion with the Protocol Chair.  Once the adverse event is Grade < 2, the 
medications may be reinstated at full dose.  If the adverse event recurs after 4 weeks, the above 
management scheme may be repeated.   
 
Subjects who develop a Grade 4 adverse event or toxicity (with the exception of asymptomatic 
laboratory abnormalities) should have all antiretroviral medication discontinued. The subject 
should be followed weekly until resolution of the adverse event and encouraged to complete the 
protocol study evaluations. Further management of antiretrovirals should proceed at the site 
investigator’s discretion. 
 
Subjects with Grade 3 or 4 asymptomatic laboratory abnormalities may continue therapy if the 
investigator has compelling evidence that the toxicity is not related to study drug, following 
discussion with the sponsor and the Protocol Chair. 
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participant due to clinical or laboratory AEs, and must stop study agent according to criteria 
defined in the safety monitoring section.   
 
13. CRITERIA FOR DISCONTINUATION 
 
13.1 PREMATURE STUDY DISCONTINUATION 
 
• 
Request by the subject to withdraw; 
• 
Request of the primary care provider if s/he thinks the study is no longer in the best 
interest of the subject; 
• 
Subject judged by the investigator to be at significant risk of failing to comply with the 
provisions of the protocol as to cause harm to self or seriously interfere with the validity 
of the study results; 
• 
At the discretion of the Ministry of Health or National Institute of Health of Peru, any of 
the IRBs/ECs responsible for oversight of the study, study sponsor, or On-Site 
Principal Investigator. 
 
13.2 PERMANENT TREATMENT DISCONTINUATION 
 
• 
Drug-related toxicity (see section 9.0 Toxicity Management); 
• 
Requirement for prohibited concomitant medications (see Section 5.3.3.); 
• 
Clinical reasons believed life threatening by the Study Medical Director, even if not 
addressed in the toxicity management of the protocol; 
• 
Suboptimal virologic response as defined in Section 4.4.; 
• 
Subject repeatedly non adherent, to the extent that the physician believes it would not 
be in the subject’s best interest to continue treatment; 
 
The subjects who permanently discontinue treatment provided by the study according to the 
criteria described should continue a different ART regimen according to the standard of care 
currently in place.  The study investigators will take necessary steps to ensure that the subjects 
continue on ART.  Counseling will be provided with special emphasis on safety, and on efficacy 
of ART options to use in the future if the participant discontinues study ART, and does not continue 
with any other antiretroviral treatment. 
 
13.3 ASSURING REPORTING OF SUSPENSION TO THE CLINICAL TRIAL 
Any action resulting in a temporary or permanent suspension of the trial will be reported to the 
assigned and responsible NIDA Program Officer and Medical Officer.  
 
 
 

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14. STATISTICAL CONSIDERATIONS 
 
14.1. PRIMARY OBJECTIVES 
 
1) To determine the relative long-term benefits of immediate vs. early vs. delayed initiation 
of ART. 
 
2) To determine the impact of high-level alcohol use on the relative long-term benefits of 
immediate vs. early vs. delayed ART initiation   
 
14.2 SECONDARY OBJECTIVES 
1) To estimate the impact of time of initiation of antiretroviral therapy on short- and long-term 
clinical and laboratory outcomes. 
 
2) To determine whether NNRTI and INSTI-based ART regimens have differential effects on 
time to HIV VL suppression and size of the latent HIV reservoir 
 
3) To determine whether NNRTI and INSTI-based ART have differential moderation of 
immune activation associated with HIV and alcohol abuse 
 
4) To evaluate the correlation between gastrointestinal dysbiosis and systemic immune 
activation in MSM with HIV and alcohol use disorders 
 
5) To evaluate the association with alcohol abuse and timing on ART initiation on 
neurocognitive function and neuro inflammation in MSM with acute and recent HIV 
 
14.3 ENDPOINTS  
 
14.3.1 Primary Endpoints 
 
1) To determine the relative long-term benefits of immediate vs. early vs. delayed initiation 
of ART. 
 
1. Measure the impact of early treatment on cell-activation, and inflammation by 
comparing cellular markers of inflammation in study participants who initiated 
treatment at varying times after HIV acquisition.   
 
2. Measure the impact of early treatment on the replication-competent HIV reservoir 
(size of the reservoir and types of cells involved) in study participants who initiated 
treatment at varying times after HIV acquisition.   
 
3. Determine whether early ART initiation prevents long-term changes in 
gastrointestinal tract bacterial microbiota and correlate these changes with 
systemic markers of inflammation and disease progression such as the activity of 
the kynurenine pathway of tryptophan catabolism and plasma concentrations of 
the inflammatory cytokines. 
 
4. Document the impact of early ART initiation on ‘non-HIV-associated’ diseases 

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such as neurocognitive disorders.  Assess the correlation of these clinical 
outcomes with laboratory markers of cell activation, inflammation and HIV reservoir 
size and characteristics. 
 
5. Determine the impact of high-level alcohol use on the outcomes listed in 1-4, after 
controlling for time of ART initiation. 
 
14.3.2 Secondary Endpoints 
1. Examine the time course of seeding of the replication-competent HIV reservoir 
quantifying the size of the reservoir and identifying the types of cells involved at 
time-points close to HIV acquisition. 
 
2. Characterize innate immune responses (cytokines and other soluble mediators) 
shortly after infection and determine the impact of these responses on the strength 
and character of the subsequent adaptive immune response to HIV, as well as the 
size and characteristics of the HIV reservoir (see above). 
 
3. Probe changes in gastrointestinal tract bacterial microbiota shortly after HIV 
infection and determine the correlation of these changes with two established 
markers of disease progression: the activity of the kynurenine pathway of 
tryptophan catabolism and plasma concentrations of the inflammatory cytokines. 
 
14.4 SAMPLE SIZE AND ACCRUAL 
 
14.4.1 MERLIN COHORT OF ACUTE AND RECENT HIV INFECTION 
Our goal is to enroll the total of participants who enrolled in the SABES step 3 study.    
 
14.4.2 MERLIN SUB-STUDIES 
40 participants will be separately consented and enrolled in sub-studies of qualitative  integration 
of HIVreservoirs (leukapheresis)  and neuro-inflammation; and 60 participants will also be 
separately consented for studies of GI microbiome (rectal biopsy/secretion).  These participants 
may choose to participate in one, two, or all of the elective evaluations which require a separate 
consent and specific procedures as outlined in this protocol and corresponding SSPs. 
 
14.5 MONITORING 
 
All endpoints will be calculated and monitored on a quarterly basis throughout the period of 
enrollment and treatment. 
 
 
 
 
 
 
 
14.6 ANALYSES  
 

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14.6.1 TESTING OF URINE, AND DRIED BLOOD SPOTS 
 
Since high-level alcohol use is an exposure of interest, detailed questionnaire data will be 
collected and biologic specimens will be analyzed at least once a year to monitor use of alcohol 
and other substances (cocaine, marijuana). 
 
14.6.2 MEASUREMENT OF THE HIV RESERVOIR 
 
It is likely that early ART prevents the establishment of the long-lived latent reservoir, and this 
hypothesis is supported by several lines of evidence. However, to date almost all studies 
investigating this question have used PCR-based assays, which overestimate the size of the 
reservoir [12] because they do not distinguish between cells with defective, replication-
incompetent cells vs. productively infected cells and the small pool of long-lived, latently infected 
cells. Conversely, the viral outgrowth assays measure only resting CD4+ T cells with replication 
competent HIV and likely underestimate the size of the reservoir [55]. Therefore, it is still unclear 
when and where the latent replication-competent reservoir is seeded.  Our collaborator, Dr. 
Nicolas Chomont, has recently developed a novel assay (Tat/Rev Induced Limiting Dilution 
Assay, “TILDA”) that can more precisely measure the frequency of productively and latently 
infected cells in a clinical sample as various times after infection. This assay measures the 
frequency of cells harboring inducible HIV without the above-mentioned limitations of standard 
assays (Figure 2). By combining ultrasensitive detection of multiply spliced (ms) RNAs upon T 
cell receptor stimulation together with a limiting dilution assay, this method allows Dr. Chomont’s 
lab to measure a frequency of cells harboring transcriptionally silent - nonetheless inducible – 
viruses. To our knowledge, this viral induction assay is the only method that allows the 
measurement of the frequency of cells harboring inducible virus that can be performed with less 
than a million CD4+ T cells.  
 
Figure 2: HIV RNA induction assay. Sorted CD4+ T cells are stimulated for 12 hours with PMA/ionomycin. Serial 
dilutions of the stimulated cells are distributed in a 96-well plate and digested. Multi-spliced HIV RNA are detected in a 
2-step real time PCR. The maximum likelihood method is used to calculate the frequency of cells with inducible HIV 
RNA based on the number of positive well. 
 
 
 
 
 
 
 
 
 
 
 
 

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14.6.3 INNATE IMMUNE RESPONSES AND INFLAMMATION 
Innate immune cells are the major drivers of the inflammation that is required to mount protective 
immune responses and mount a rapid response after HIV acquisition [14]. The innate immune 
cells involved in this response are diverse in their phenotypes and functions.  Cytokines secreted 
by these cells influence the maturation and development of effector cells that drive humoral and 
cellular immune responses to HIV. Molecular interactions of these cells with cells of the adaptive 
immune system also impact quantitative and qualitative features of primary and recall immune 
responses.  It is likely that the balance among immune modulating factors induced shortly after 
HIV acquisition determines the strength and character of the adaptive immune response to 
infection as well as the size and characteristics of the HIV reservoir. 
 
Using multiparameter flow cytometry we will: 1) enumerate T cells, B cells, monocytes, myeloid 
dendritic cells, plasmacytoid dendritic cells; and 2) perform in depth immunophenotyping of T 
cells, including markers of maturation (e.g., CD45RO/CD27), differentiation (e.g., into TH1, TH2, 
TH17, and/or Treg subsets), activation (e.g., Ki67, CD38, HLA-DR, and/or PD-1), and cytokine 
production (e.g., of IL-2, -4, -7, -16, TNF, and IFNγ). In addition, using plasma samples, we will 
measure markers of chronic inflammation (e.g., CRP, D-dimer, sCD14, and an array of 
chemokines and cytokines) using commercially available ELISA kits and multiplex assays, as well 
as activity of the immunomodulatory kynurenine pathway of tryptophan catabolism 
[kynurenine:tryptophan ratio] using LC-MS/MS as described previously. In addition, our 
collaborators, Drs. Rafick Sekaly and Mark Cameron, will use transcriptional profiling to measure 
changes in innate immune responses, cell activation markers and inflammatory mediators 
associated with HIV acquisition and in response to HIV infection and ART treatment.  RNA-Seq 
transcriptomic profiling in his laboratory will provide an unbiased and sensitive tool to evaluate 
immune responses.  This comprehensive approach will include the quantitative and qualitative 
assessment of the multiple pro- and anti-inflammatory pathways and their regulation; these 
parameters are not generated when performing conventional assays to measure cytokines. 
14.6.4 DYSBIOSIS OF THE GUT MICROBIOTA AND CORRELATION WITH MARKERS OF 
HIV-ASSOCIATED IMMUNOPATHOLOGY. 
Early HIV-associated damage to gastrointestinal mucosa and subsequent translocation of 
microbial products into the systemic circulation are thought to play a central role in the 
inflammatory changes associated with AIDS and non-AIDS related morbidities. Recent studies 
have shown that untreated HIV-infected subjects exhibit dysbiosis - a markedly different 
composition of the gut bacterial microbiota [19, 56]. This dysbiosis persists in some during ART, 
and the extent of dysbiosis correlates with activity of the kynurenine pathway of tryptophan 
catabolism and plasma concentrations of the inflammatory cytokine interleukin-6 (IL-6), two 
established markers of disease progression.  
 
Stool specimens taken during untreated acute/recent infection, and after ART initiation will be 
processed and submitted to 16S rRNA-based phylogenetic characterization of microbiome 
composition in the laboratory of our collaborator, Dr. Susan Lynch. DNA will be extracted from 
stool and rectal biopsy/secretion samples using a protocol optimized for the isolation of bacterial 
DNA [57]. Exploratory data analyses will seek to identify operational taxonomic units (OTUs) that 
change in abundance as a result of acute HIV infection and to determine whether the abundance 
of such OTUs is linked to markers of immune activation and viral reservoir seeding. Furthermore, 
comparisons of the composition of distinct microbial community samples will be utilized to 
understand if initiation of early ART is associated with a gut microbiota that more resembles the 

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pre-infection state as compared to microbiota from subjects who initiate ART later after HIV 
acquisition. Multiple specimens from the same participant will be analyzed to assess how the 
timing of initiation of ART affects the long-term make-up of the GI microbiome. Urine will also be 
used to examine microbiome function through measurement of urinary metabolites.  
 
14.6.5 DNA INTEGRATION SITES  
Drs. Frenkel and Mullins will characterize and compare the HIV DNA integration sites in subjects 
with and without high-level alcohol use who started ART in Fiebig stages I-II, FIII-V and in the 
deferred ART arm. Among participants with sustained suppression of HIV RNA to undetectable 
levels, a total of 45 participants (~15 subjects from each group) will be studied upon enrollment 
(prior to the initiation of ART), and after 3.5 years of ART. PBMC from the subset of participants 
agreeing to leukapheresis will be preferentially selected for these studies. 
 
14.6.6 NEUROLOGIC AND NEUROCOGNITIVE EFFECTS 
We will use bi-annual neurocognitive testing to determine whether a) early ART initiation during 
acute or recent infection prevents cognitive decline and b) alcohol use during acute infection 
accelerates early cognitive decline caused by HIV.  To determine the impact of early ART initiation 
and alcohol use on HIV infection in the CNS, neuronal injury and neuro-inflammation we will 
conduct analyses of cerebrospinal fluid (CSF) in a subset of 40 participants. These include 
measures of brain infection (CSF/blood viral load ratio), inflammation (soluble markers in 
blood/CSF) and injury (CSF markers of axonal degeneration) in subjects with and without alcohol 
use disorder at baseline and during follow-up. 
 
15. DATA COLLECTION, MONITORING, AND ADVERSE EXPERIENCE REPORTING 
 
15.1 DATA COLLECTION 
Data collection in the MERLIN study will use the same questionnaires used for HIV+ participants 
in the SABES study.  In addition, collection of medical data including medical record review, 
routine laboratory results, and results of routine and study-specific medical procedures (including 
laboratory tests, neurocognitive tests) will follow procedures established in the SABES study. 
Collection of biologic specimens will include blood collection for PBMC (peripheral blood 
mononuclear cells), plasma and serum, urine, GI biopsies and stool. Because drug and alcohol 
use are common among HIV-infected individuals and individuals at high risk of HIV infection, we 
will collect detailed information on drug and alcohol use as well as collecting dried blood spots, 
hair and urine for tests for drug and alcohol metabolites. 
 
Stored blood samples will be used in assays measuring the HIV reservoir (size and cellular 
location), and biologic responses to HIV infection and ART treatment including measures of cell 
activation, markers of inflammation, innate immune cell signaling and induced immune responses. 
Stool samples will be collected for assessment of the gastrointestinal microbiome to support 
studies of HIV-induced dysbiosis and how the microbiome influences systemic inflammatory 
markers thought to play a prominent role in HIV immunopathogenesis. HIV viral load will be 
monitored in plasma. Specimens will be used for development of new assays for detections of 
early HIV infection; this will involve plasma at a minimum but may involve additional specimen 
types as well. 
 

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15.2 DEFINITION OF AN ADVERSE EVENT 
An adverse event (AE) is defined as any untoward medical occurrence in a clinical research 
participant who has been administered an investigational product, and that does not necessarily 
have a causal relationship with the investigational product.  As such, an AE can be an unfavorable 
or unintended sign (including an abnormal laboratory finding, for example), symptom, or disease 
temporally associated with the use of an investigational product, whether or not considered 
related to the product.  This definition will be applied to both study treatment groups, even though 
one group is assigned to receive an investigational product immediately and the other not, and 
will be applied to both groups beginning from the time of random assignment. 
 
Study participants will be provided instructions for contacting the study site to report any untoward 
medical occurrences they may experience, except for possible life-threatening events, for which 
they will be instructed to seek immediate emergency care.  Where feasible and medically 
appropriate, participants will be encouraged to seek evaluation where the study clinician is based, 
and to request that the clinician be contacted upon their arrival.  With appropriate permission of 
the participant, and whenever possible, records from all non-study medical providers related to 
untoward medical occurrences will be requested and required data elements will be recorded on 
study case report forms and/or in the participant’s medical chart. 
 
15.3 GOVERNANCE 
The Protocol Chair is ultimately responsible for adherence to all aspects of the study protocol, 
including reporting of AEs.  This responsibility is largely delegated to the On-Site Principal 
Investigator, who is responsible for medical decisions.  He or his authorized study physicians (all 
of them trained in internal medicine and/or infectious diseases) will prepare all AE reports.  In 
addition, there is real-time data checking by the data management unit at the study site, which 
will review data collection forms, including clinic and laboratory reports, from all participants.  The 
review will serve to assure that evidence of AEs is identified and reported. 
 
A Protocol Safety Review Committee will review AE reports and determine appropriate follow-up, 
including modifying the study protocol and/or procedures as necessary. 
 
15.4 ASSESSMENT OF AE RELATIONSHIP TO STUDY AGENT 
The on-site Principal Investigator or his designee will assess whether an AE is related or not 
related to the study agent, using the available information about co-formulated 
elvitegravir/cobicistat/emtricitabine/tenofovir 
disoproxil 
fumarate, 
co-formulated 
elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide,and his/her clinical judgment. 
 
The anticipated risks associated with this study are deemed overall to be low.   
 
The assessment of risk does not, however, preclude the potential for anticipated and/or 
unanticipated AEs, serious or otherwise, since it is not possible to predict with certainty the 
absolute risk in any given individual or in advance of first-hand experience with the proposed 
study methods. 
 
We will use a Data Safety Monitoring Plan (DSMP) to monitor the overall progress of our study.  
Some of the factors the investigators intend to monitor closely include: 1) Are the treatment groups 
comparable at baseline; 2) Are the accrual rates meeting initial projections and is the trial on its 

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scheduled timeline; 3) Are the data of sufficient quality; 4) Are the treatment groups different with 
respect to safety and toxicity data; 5) Are the treatment groups different with respect to efficacy 
data; 6) Is there an indication to discontinue the trial due to predefined criteria; and 7) Should the 
protocol be modified in response to any unanticipated outcome or change in temporal event?. 
 
15.5 FOLLOW-UP OF ADVERSE EVENTS 
All participants reporting an untoward medical occurrence will be followed clinically until the 
occurrence resolves (returns to baseline) or stabilizes.  Laboratory AEs will be managed 
according to established protocols described in 9.0 Toxicity Management. Laboratory results that 
require action will be documented and a peer navigator will be contacted to schedule a repeat 
visit.   
 
15.6 EXPEDITED ADVERSE EVENTS REPORTING TO NATIONAL INSTITUTE OF DRUG 
ABUSE 
The expedited adverse event (EAE) reporting requirements and definitions for this study and the 
methods for expedited reporting of AEs to the NIDA will be based on “The Manual for Expedited 
Reporting of Adverse Events to DAIDS Version 2.0” dated in January 2010.  This manual is 
available on http://rsc.tech-res.com/safetyandpharmacovigilance.  Adverse events reported on an 
expedited basis must be documented on the 2010 NIDA Serious Adverse Event form and reported 
to the NIDA Program Official within 72 hours by fax (1-301-443-6814) and/or email.  Investigators 
will submit a written report to the NIDA Program Official no more than three days after site aware.  
Written follow-up will be sent to the NIDA Program Official   
 
This study uses the standard level of EAE reporting.  In addition, the On-Site Principal Investigator 
will submit AE information as required by local regulatory or other relevant authorities. 
 
15.6.1 Study Agents for Expedited Reporting to National Institute on Drug Abuse Program Official 
 
The study drugs on which the relatedness assessment to be based are co-formulated 
elvitegravir/cobicistat/emtricitabine/tenofovir 
disoproxil 
fumarate 
or 
elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide and reported to the NIDA Program 
Official. 
 
15.6.2 Grading Severity of Events 
 
All AEs will be graded using the “Division of AIDS Table for Grading the Severity of Adult and 
Pediatric Adverse Events Version 1.0, December, 2004; Clarification August 2009” available at 
http://rsc.tech-res.com/safetyandpharmacovigilance. 
 
15.6.3 Adverse Events Reporting Periods 
 
Adverse events must be reported on an expedited basis at the Standard Level during the protocol-
defined EAE reporting period, which is: The entire study duration for an individual subject (from 
study enrollment until study completion or discontinuation of the subject from study participation 
for any reason).  After the end of the protocol-defined EAE reporting period stated above, the 
study site must report serious, unexpected, clinically suspected AE drug reactions if the study site 
staff becomes aware of the event on a passive basis, i.e., from publicly available information. 

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15.7 CONTACT FOR QUESTIONS ABOUT EXPEDITED ADVERSE EVENTS 
For questions about EAE reporting, contact NIDA Program Official sending an e-mail.  
 
15.8 SOCIAL ADVERSE EVENTS 
This study will be designed to minimize risk and maximize benefit to both study participants and 
their local communities.  However, volunteers could experience discrimination or other personal 
problems as a result of being in the study.  We will provide advocacy for and assistance to 
participants regarding negative social impacts or social AEs associated with the study.   
 
Social AEs may include loss of privacy, stigmatization, interference with gainful employment, and 
coercion.  Information regarding social AEs will be solicited during quarterly study visits after 
enrollment in the study and will be recorded in log form on case report forms.  In addition, social 
harms may be identified by other study staff, including peer navigator, patient advocates, nurses, 
physicians, pharmacists, and others.  All social adverse events will be brought to the attention of 
the Study Medical Director and reported according to AE reporting guidelines.  Participants who 
report social harms will be referred to speak with a social worker and/or a study counselor. 
 
16. HUMAN SUBJECTS PROTECTION 
 
16.1 INSTITUTIONAL REVIEW BOARDS AND ETHICS COMMITTEE REVIEW  
This protocol and the informed consent forms and any subsequent modifications will be reviewed 
and approved by the IRB or ethics committee responsible for oversight of the study.  Signed 
consent forms will be obtained from the subject.  The consent forms will describe the purpose of 
the study, the procedures to be followed, and the risks and benefits of participation.  A copy of 
the consent forms will be given to the subject, and this fact will be documented in the subject’s 
record. 
 
16.2 SUBJECT CONFIDENTIALITY 
All laboratory specimens, evaluation forms, reports and other records that leave the site will be 
identified by coded number only to maintain subject confidentiality.  All records will be kept locked.  
All computer entry and networking programs will be done with coded numbers only.  Clinical 
information will not be released without written permission of the subject, except as necessary for 
monitoring by the Ministry of Health or National Institute of Health of Peru, any of the IRBs/ECs 
responsible for oversight of the study, or the NIDA. 
 
16.3 STUDY DISCONTINUATION 
The study may be discontinued at any time by the Ministry of Health or National Institute of Health 
of Peru, any of the IRBs/ECs responsible for oversight of the study, or NIDA as part of their duties 
to ensure that research subjects are protected.  
 
 

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17. PUBLICATIONS OF RESEARCH FINDINGS 
 
Presentation and publication of the results of this study will follow the regulations of Fred 
Hutchinson Cancer Research Center and Asociacion Civil Impacta Salud y Educacion.  Any 
presentation, abstract, or manuscript must be approved by the Protocol Chair prior to submission. 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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Amendment letter 1 
Page 1 of 1 
July 31 2018 
Amendment Letter N° 01 
Date 
: July 31 2018 
To 
: Research Protocol Team 
From 
: Protocol Chair and Co-Chair 
Topic 
: Amendment letter N° 1 to MERLIN Protocol, Version 3.0, April 12 2018, 
entitled “Modulating the Impact of Critical Events in Early HIV Infection: Effect 
of ART Initiation and Alcohol use”.  
This amendment letter will be sent to the respective Ethics Committees.  Each site will need 
to file a copy of this amendment letter together with the protocol of reference. The 
amendments contained in this letter must be implemented immediately after approval by the 
Peruvian National Institute of Health.  These updates will be included in the next version of 
the protocol if applicable.  
The changes proposed in this letter are aligned with the main primary and secondary 
objectives of the study protocol, which are not being modified.   
•
Section 10.3.3 Last study visit. This section has been amended to include termination
of participants by consideration of the protocol team, it now reads:
The last study visit will not be a specific numeric visit, but will occur before or by December 31 
2022.  All participants will be followed for approximately 5 years independently of the interval 
between the SABES and MERLIN studies, with the exception of those participants who, by the 
protocol team decision, must be terminated (having a shorter follow up time).  
•
Section 13.1 Premature termination from the study. A new category has been added,
it now reads:
o
Protocol team request, analysis participant data/specimens will not be important of
the study evaluation (they will not be relevant for the statistical analysis).
•
Section 13.4 Follow-up of participants without specimen collection different from
the required for safety labs to evaluate treatment.  This section has been included to
describe the follow-up of participants for whom the different specimen collections for
storage will be no longer done, it now reads:
Participants who by protocol team evaluation are in the following categories: 
•
Without antiretroviral treatment for a period longer than 3 months; however having
undetectable viral load values
•
Viral load levels  >1000 copies/mL without treatment interruption (good adherence)
•
Do not have PBMC, stool, urine, CSF since HIV diagnosis
IRO REC'D 01/22/2021
FHCRC IRB Approval  
FEB 11 2021 
Document Released Date

Amendment letter 2 
Page 1 of 2 
March 01 2019 
Amendment Letter N° 02 
Date 
: March 01 2019  
To 
: Research Protocol Team 
From 
: Protocol Chair and Co-Chair 
Topic 
: Amendment letter N° 2 to MERLIN Protocol, Version 3.0, April 12 2018, 
entitled “Modulating the Impact of Critical Events in Early HIV Infection: Effect 
of ART Initiation and Alcohol use”.  
This amendment letter will be sent to the respective Ethics Committees.  Each site will need 
to file a copy of this amendment letter together with the protocol of reference. The 
amendments contained in this letter must be implemented immediately after approval by the 
Peruvian National Institute of Health.  These updates will be included in the next version of 
the protocol if applicable.  
The changes proposed in this letter are aligned with the main primary and secondary 
objectives of the study protocol, which are not being modified.   
•
Section 10.3.4.10 Leukapheresis. This section has been amended to increase the
number of participants that could undergone the procedure, it now reads:
All the study participants could be invited to undergo leukapheresis.  Based on operational and 
budget considerations it was initially considered to include only 40 participants for this 
procedure. However, we have lost participants who initially had accepted to undergo this 
procedure, because they are no longer eligible to continue in the study or because they refuse 
to continue in the procedure for personal reasons.  
This modification will allow replacement of participants who could have been lost to follow-up 
in MERLIN, and include additional participants who are eligible for these procedures.  This will 
allow a more robust analysis at the late time points of the study.  
Participants will be invited to participate in this procedure according to their antiretroviral 
treatment initiation condition and clinical evolution.  
There is a separate informed consent.  The qualitative and quantitative evaluation of HIV 
seeding (including its location in different CD4+ T cells subsets) will require a big number of cells, 
and it is important to learn about the size and distribution of the HIV reservoir, this is a key 
factor to induce a functional cure.  Hence, we will use leukapheresis to collect a big number of 
cells at specific times (weeks 72, 120, 168 and 216 for the deferred arm and weeks 96, 144, and 
192 for the immediate arm).  
•
Section 10.3.4.14 Lumbar Puncture. This section has been amended to increase the
number of participants that could undergone the procedure, it now reads:
All the participants could be invited to undergo lumbar puncture.  Based on operational and 
budget considerations it was initially considered to include only 40 participants for this 
procedure. However, we have lost participants who initially had accepted to undergo this 
IRO REC'D 01/22/2021
FHCRC IRB Approval  
FEB 11 2021 
Document Released Date

Amendment letter 2 
 
Page 2 of 2 
March 01 2019 
procedure, because they are no longer eligible to continue in the study or because they refuse 
to continue in the procedure for personal reasons.  
This modification will allow replacement of participants who could have been lost to follow-up 
in MERLIN, and include additional participants who are eligible for these procedures.  This will 
allow a more robust analysis at the late time points of the study.  
Participants will be invited to participate in this procedure according to their antiretroviral 
treatment initiation condition and clinical evolution.  
Those participants who accept the procedure will need to sign a specific informed consent; 
otherwise, no procedure could be performed. The evaluations will be done at specific visits 
indicated in the procedures table.  
 

Carta de Enmienda 3 
Página 1 de 2 
01 de diciembre de 2019 
Amendment Letter N° 03 
Date 
: December 1 2019 
To        : Protocol Research Team 
From : Protocol Chair and Co-Chair 
Topic   :Amendment Letter N° 3 to Protocol MERLIN, Version 3.0, April 12 2018, entitled 
“Modulating the Impact of Critical Events in Early HIV Infection: Effect of ART 
Initiation and Alcohol use”.  
This amendment letter will be sent to the respective Ethics Committees.  Each site will need 
to file a copy of this amendment letter together with the protocol of reference. The 
amendments contained in this letter must be implemented immediately after approval by the 
Peruvian National Institute of Health.  These updates will be included in the next version of 
the protocol if applicable.  
The changes proposed in this letter are aligned with the main primary and secondary 
objectives of the study protocol, which are not being modified.   
•
Section 1.1.2. Asociación Civil Impacta Salud y Educación.  This section has been
modified to update the local study coordination, it now reads  (insertion in bold):
Maria Mamani, CNM
Study Coordinator
IMPACTA PERU Clinical Trials Unit
Asociación Civil Impacta Salud y Educación
Av. Almirante Miguel Grau No. 1010. Lima 4, Peru.
Phone: +51-1-206-7800 Ext 209
e-mail address: mmamani@impactaperu.org
•
Section 10.1. VISIT PROGRAM.  This has been modified to update, based on
considerations explained below, that in the annual visits (every 48 weeks) after week 192
for participants assigned to the immediate arm, and after week 216 for those assigned to
initiate deferred treatment (both, after diagnosis of acute  HIV infection):
1. Analysis of CD4+/CD8+ T cell subpopulations will not be performed
2. No PBMC collection will be performed
3. The volumen of blood to be collected in such visits has been updated (97 mL instead of
250 mL)
These changes bring as a consequence the modification of the informed consent: 
“Informed Consent to be enrolled in the MERLIN study”.  
•
Section  10.1. VISIT PROGRAM.  This section has been modified to update, based on
considerations described below, that in the bi-annual visits after week 192 for participants
assigned to the immediate arm, and after week 216 for those assigned to initiate deferred
treatment (both, after diagnosis of acute  HIV infection):
1. Analysis of CD4+/CD8+ T cell subpopulations will not be performed
These changes bring as a consequence the modification of the informed consent: 
“Informed Consent to be enrolled in the MERLIN study”. 
IRO REC'D 01/22/2021
FHCRC IRB Approval  
FEB 11 2021 
Document Released Date

 
Carta de Enmienda 3 
 
Página 2 de 2 
01 de diciembre de 2019 
 
• 
Section  10.3.4.8. Immunologic Studies, item 1. CD4+/CD8+ T-cell subsets. It has been 
modified to describe the most current medical care standard offered to people living with 
HIV in our country, it now reads (insert in bold): 
 
A CD4+ T-lymphocyte percent of total lymphocytes and CD8+ T-lymphocyte percent of 
total lymphocytes should be performed in addition to the absolute CD4+ and CD8+ T cell 
counts at screening and for all visits at which CD4+/CD8+ T cell counts are required.  
Because of the diurnal variation in CD4+ and CD8+ cell counts, determinations for 
individual subjects should be obtained consistently in either the morning or the afternoon 
throughout the study, if possible. 
 
As described in the most current “Technical Standard of Health for 
Comprenhensive Care of Adults living with Human Deficiency Virus” of the Peruvian 
Ministry of Health dated 2018, the evaluation of CD4+/CD8+ subsets is not 
considered as part of the standard medical care offered to people living with HIV 
under stable antiretroviral treatment, because it is a priority to monitor levels of HIV-
1 RNA in plasma for its impact determining alternative therapies in the absence of 
viral suppression.  Based on technical, operational and budget considerations, 
during the annual and bi-annual visits after week 192 for participants assigned to 
the immediate antiretroviral treatment initiation arm and after week 216 for those 
assigned to initiate deferred antiretrovrial treament (both after being diagnosed with 
acute HIV infection), no evaluation of CD4+/CD8+ subsets will be performed, unless 
there is a justified medical indication to perform such evaluation.   
 
NOTE: Each time a CD4+/CD8+ measurement is obtained, the local laboratory must 
perform a  WBC and differential from a sample obtained at the same time. 
 
• 
Section 10.3.4.11 Stored Plasma, PBMC and Whole Blood in RNA Later.  It has been 
modified to indicate that PBMC will not be collected in the respective visits, based on 
operational and budget considerations, it now reads (insertions in bold):   
 
At all time points, whole blood, plasma, and PBMC will be stored for later analysis, many 
of which are described in the analysis plan, or else are for future studies as per 
specimen repository consents. 
Based on technical, operational and budget considerations, during the annual and 
bi-annual visits after week 192 for participants assigned to the immediate 
antiretroviral treatment initiation arm and after week 216 for those assigned to 
initiate deferred antiretroviral treatment (both after being diagnosed with acute HIV 
infection), no PBMC collection will be collected, because it will not contribute with 
the evaluation of the main study objectives which is planned for years 2 and 4 after 
initiation of antiretroviral treatment.