Accurate Staging of Immuno-virological Dynamics During Acute HIV Infection
Conditions: HIV, Seroconversion, HIV
Sponsor: University Hospital, Ghent

 
 
Protocol, version I, dd. 25/01/2018 
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Study protocol 
Accurate staging of immuno-virological dynamics during acute 
HIV infection  
 
Sponsor: UZ Gent  
Principal Investigator: Prof Linos Vandekerckhove 
Department of General Internal Medicine 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
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Co investigators: 
 
Prof. Dr. Chris Verhofstede and Dr. Virginie Mortier 
Aids Referentie labo UGent 
 
Els Caluwé and Sophie Vanherreweghe 
Algemene inwendige ziekten,  UZGent 
Study nurses 
 
Dr. Nathalie Van der Moeren  
Algemene inwendige ziekten, UZGent 
 
Dr. De Scheerder Marie-Angélique 
Algemene inwendige ziekten, UZGent  
 
Prof. Dr. Annemieke Dhondt  
Nierziekten, UZGent  
 
Prof. Dr. Frank Vermassen 
Thoracale en vasculaire heelkunde, UZGent  
 
Prof. Dr. De Looze Danny 
Gastro-enterologie, UZGent  
 
Prof. Dr. Coppens Marc  
Anesthesie, UZGent  
 
Dr. Van Wanzeele Filip, 
Algemene inwendige ziekten,  UZGent 
 
Dr. Pelgrom Jolanda,  
Algemene inwendige ziekten,  UZGent 
 
Dr. Van Der Gucht Bea,  
Algemene inwendige ziekten,  UZGent 
 
Prof. Dr. Stevens Callens  
Algemene inwendige Ziekten, UZ Gent  
 
Dr. Diana Huis in ’t Veld 
Algemene Inwendige Ziekten, UZ Gent  
 
Dr. Magdalena Sips 
HIV Cure Research Center, UGent 

 
 
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Dr. Eva Malatinkova 
HIV Cure Research Center, UGent 
 
Karen Vervisch 
HIV Cure Research Center, UGent 
 
Prof. Dr. Dirk Vogelaers,  
Diensthoofd Algemene Inwendige Ziekten  
 
Departments/laboratories involved:  
Department of Internal Medicine, Infectious Diseases and Psychosomatic Medicine, Ghent University 
Hospital  
Department of Gastroenterology, Ghent University Hospital  
Department of Anaesthesia, Ghent University Hospital  
Department of thoracic and vascular surgery, Ghent University Hospital  
Department of nephrology, Ghent University Hospital  
Aids Referentie lab, Department of Clinical chemistry, microbiology and immunology. 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
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1. OBJECTIVE OF THE STUDY  
 
1.1 GOAL OF THE STUDY 
 
This study will evaluate how immunological and virological profiles of the different anatomical 
compartments evolve in patients before and after treatment initiation in individuals starting treatment 
during acute HIV seroconversion. Monitoring of immune parameters will allow us to assess the presence 
of chronic inflammation and immune exhaustion in subjects that start treatment in early stage of infection 
as compared to those who start treatment in the chronic phase of infection. Additionally, we aim to 
evaluate how early treatment affects composition of gut microbiota and how that is linked to immune 
homeostasis in gut-associated lymphoid tissue (GALT). By this longitudinal study design, we will be able 
to assess if and how the viral reservoir, established during early infection stages, evolves during the 
course of infection, while patients remain on combination anti-retroviral therapy (cART). Comparing blood 
and tissue compartments at different stages of infection will assess compartmentalisation of the reservoir. 
 
1.2 HYPOTHESIS 
 
We hypothesize that the magnitude of innate immune responses at different stages of acute HIV infection 
is directly linked to the strength of antigenic stimulation and impacts the development of adaptive immune 
responses. We further hypothesize that the initial viral load burden (linked to the degree of antigenic 
stimulation) impacts the reservoir size and therefore the immunological and virological profile of the 
patients is directly linked to the different stage of infection. Given that HIV has strong tropism to the GALT 
and does severe damage to the intestinal mucosal system early in infection, we hypothesize that early 
treatment initiation will allow for the maintenance of gut epithelial integrity and therefore GALT and gut 
microbiome homeostasis. Furthermore, we believe that the size and anatomical localization of the 
reservoir is directly correlated to the stage at treatment initiation. If this is the case, accurate staging will 
provide an invaluable tool to compose specific patient cohorts for HIV cure studies in the future. We will 
use Fiebig staging or more accurate staging if this becomes available. 
 
1.3 RATIONALE 
 
Human immunodeficiency virus (HIV) is the causative agent of the acquired immunodeficiency syndrome 
(AIDS). The world health organisation (WHO) has estimated that 78 million people have been infected 
since the beginning of the HIV pandemic, and 35 million people have died from AIDS1. Today, 
approximately 37 million people are still infected with HIV-1, out of which 17 million are currently on 
combined antiretroviral therapy (cART)1. Since its development, cART has saved and increased the 
quality of millions of peoples’ lives. Although, the treatment efficiently supresses viral replication and 
prevents progression to AIDS, current cART regiments are not able to eliminate the latent viral 
reservoir that is established within the first days of infection2,3. This reservoir is responsible for viral 
rebound at treatment interruption4. 
One of the major disadvantages of cART is chronic treatment necessity. The burden of chronic treatment, 
along with treatment costs, difficulties to access treatment in some parts of the world and ongoing chronic 
inflammation despite viral suppression, create an urgent need for a cure. For the vast majority of 

 
 
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patients, a sterilising cure (complete elimination of the viral reservoir) is not feasible. Therefore, the focus 
is on a functional cure or the so-called “HIV remission” by achieving a substantially small viral reservoir 
that can be spontaneously controlled by immune system without the need of cART. Although this has 
been achieved in a small group of patients, immunological processes behind it are not well understood5. 
So far, only early cART initiation has proven a positive effect on limiting the size of the viral reservoir6–
8. Recent HIV-cure trials have been performed on chronically infected patients that started therapy 
late in a chronic phase of infection and have not been able to show an effect on the size of the reservoir. 
Instead of using patients with such heterogeneous viral reservoirs, we believe that these trials should 
first be performed on a cohort of patients with a well-characterised, small HIV reservoir, who are 
close to a functional cure. We believe that Fiebig staging (Figure 1, below) forms a suitable tool to 
define such cohort, but in order to validate the value of these stages, we need to investigate whether or 
not they are well correlated with the immune, virological and microbiome parameters in early cART 
initiated patients. 
Fiebig stages have been characterised by Fiebig et al.9, using markers that allow for precise “serum 
based” staging of HIV infection. As shown in the research methodology, the first stage is characterised 
by the presence of viral RNA (stage I), subsequent stages are characterised by the presence of p24 
antigens (stage II); p24 antibodies (stage III); and increasingly specific Western blot patterns (stage IV – 
VI)9,10. It is currently not known how immune responses and viral reservoir development in the 
different anatomical compartments are linked to these Fiebig stages.  
 
 
 
Figure 1: Laboratory staging of HIV 
infection. The first four Fiebig stages 
are characterised by the subsequent 
detection of viral RNA, p24 antigen, 
antibodies and a semi-positive 
western blot (some, but not all bands 
are present). (McMichael et al., 201029). 
 
 
 
 
First, we aim to perform in-depth profiling of immune responses initiated in acute infection at 
different Fiebig stages to understand which specific immune responses are the most efficient in 
restricting the establishment of viral reservoir in different anatomical tissues.  
Primary HIV infection is characterized by an increase in the levels of acute-phase proteins, as well as a 
cytokine storm, activation of the complement system and a rapid rise in plasma viremia11. The earliest 
innate immune responses include: formation of neutrophil extracellular traps, activation and decline in 
numbers of dendritic cells12,13 and activation of natural killer and natural killer T cells14–16. Chronic HIV 
infection is characterised by chronic immune activation, which leads to persistent inflammation17 and 
immune exhaustion18,19. Mainly virus-specific CD8 T cells undergo functional exhaustion, lose effector 
functions and fail to control viral infection20. 

 
 
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Most of the acute HIV infection studies have been conducted during the decline of viral load. Recently, 
magnitude and kinetics of CD8 T cell activation have been evaluated during hyperacute HIV infection21, 
however, precise in-depth characterization of innate immune responses at different Fiebig stages 
and how these are linked to the establishment of adaptive immune responses have not been 
performed.  
Although cART-mediated viral suppression causes significant reductions, many immune activation 
pathways remain abnormal during suppressive cART, especially in patients who initiated cART during 
later infection stages. We believe that chronic inflammation and immune exhaustion will be 
prevented by early treatment initiation.  
Integration of viral DNA into the host resting CD4 T cell genome has been shown to occur during early 
infection and leads to the formation of a very stable latent viral reservoir22–24. In-depth analysis of viral 
reservoir dynamics will allow us to determine if infection of different cell subsets occurs in a similar 
manner in blood and anatomical compartments and if the Fiebig stages can be used as a tool for 
the prediction of infected CD4 T cell subsets. In addition, we aim to map how seeding of the viral 
reservoir occurs in different anatomical compartments in vivo and how this reservoir evolves under 
treatment. Recent data have shown residual levels of continuous virus production in lymphatic 
tissues25,26, which may be responsible for constant replenishment of the viral reservoir26. 
Lastly, analysis of microbiome composition will allow us to determine impact of HIV infection and early 
treatment on gut microbiome composition that is inherently linked to GALT integrity and immune 
activation. 
 
References:  
1. 
UNAIDS. Global Aids Update. (2016). 
2. 
Chun, T.-W., Moir, S. & Fauci, A. S. HIV reservoirs as obstacles and opportunities for an HIV cure. Nat. 
Immunol. 16, 584–589 (2015). 
3. 
Whitney, J. B. et al. Rapid seeding of the viral reservoir prior to SIV viraemia in rhesus monkeys. Nature 
512, 74–77 (2014). 
4. 
Chun, T. W., Davey, R. T., Engel, D., Lane, H. C. & Fauci, A. S. Re-emergence of HIV after stopping 
therapy. Nature 401, 874–5 (1999). 
5. 
Sáez-Cirión, A. et al. Post-Treatment HIV-1 Controllers with a Long-Term Virological Remission after the 
Interruption of Early Initiated Antiretroviral Therapy ANRS VISCONTI Study. PLoS Pathog. 9, (2013). 
6. 
Ananworanich, J., Dubé, K. & Chomont, N. How does the timing of antiretroviral therapy initiation in acute 
infection affect HIV reservoirs? Curr. Opin. HIV AIDS 10, 18–28 (2015). 
7. 
Malatinkova, E. et al. Impact of a decade of successful antiretroviral therapy initiated at HIV-1 
seroconversion on blood and rectal reservoirs. Elife 4, 1–17 (2015). 
8. 
Laanani, M. et al. Impact of the timing of initiation of antiretroviral therapy during primary HIV-1 infection on 
the decay of cell-associated HIV-DNA. Clin. Infect. Dis. 60, 1715–1721 (2015). 
9. 
Fiebig, E. W. et al. Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications 
for diagnosis and staging of primary HIV infection. AIDS 17, 1871–9 (2003). 
10. 
Cohen, M. S., Gay, C. L., Busch, M. P. & Hecht, F. M. The detection of acute HIV infection. J Infect Dis 
202, S270-277 (2010). 
11. 
Stacey, A. R. et al. Induction of a striking systemic cytokine cascade prior to peak viremia in acute human 
immunodeficiency virus type 1 infection, in contrast to more modest and delayed responses in acute 
hepatitis B and C virus infections. J. Virol. 83, 3719–33 (2009). 
12. 
Killian, M. S., Fujimura, S. H., Hecht, F. M. & Levy, J. A. Similar changes in plasmacytoid dendritic cell and 
CD4 T-cell counts during primary HIV-1 infection and treatment. AIDS 20, 1247–1252 (2006). 
13. 
Almeida, M., Cordero, M., Almeida, J. & Orfao, A. Different subsets of peripheral blood dendritic cells show 
distinct phenotypic and functional abnormalities in HIV-1 infection. AIDS 19, 261–271 

 
 
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14. 
Alter, G. et al. Evolution of innate and adaptive effector cell functions during acute HIV-1 infection. J. Infect. 
Dis. 195, 1452–1460 (2007). 
15. 
Borrow, P. & Bhardwaj, N. Innate immune responses in primary HIV-1 infection. Curr. Opin. HIV AIDS 3, 
36–44 (2008). 
16. 
Clay, C. C. et al. Neuroinvasion of fluorescein-positive monocytes in acute simian immunodeficiency virus 
infection. J. Virol. 81, 12040–12048 (2007). 
17. 
Keating, S. M., Javobs, E. S. & Norris, P. J. Soluble mediators of inflammation in HIV and their implications 
for therapeutics and vaccine development Sheila. Cytokine Growth Factor Rev. 23, 193–206 (2012). 
18. 
Porichis, F. & Kaufmann, D. E. Role of PD-1 in HIV pathogenesis and as target for therapy. Curr. HIV/AIDS 
Rep. 9, 81–90 (2012). 
19. 
Sciaranghella, G., Tong, N., Mahan, A. E., Suscovich, T. J. & Alter, G. Decoupling activation and exhaustion 
of B cells in spontaneous controllers of HIV infection. AIDS 27, 175–180 (2013). 
20. 
Velu, V., Shetty, R. D., Larsson, M. & Shankar, E. M. Role of PD-1 co-inhibitory pathway in HIV infection 
and potential therapeutic options. Retrovirology 12, 14 (2015). 
21. 
Ndhlovu, Z. M. et al. Magnitude and Kinetics of CD8+ T Cell Activation during Hyperacute HIV Infection 
Impact Viral Set Point. Immunity 43, 591–604 (2015). 
22. 
De Rijck, J., Vandekerckhove, L., Christ, F. & Debyser, Z. Lentiviral nuclear import: A complex interplay 
between virus and host. BioEssays 29, 441–451 (2007). 
23. 
Siliciano, R. F. & Greene, W. C. HIV latency. Cold Spring Harb. Perspect. Med. 1, 1–20 (2011). 
24. 
Siliciano, J. D. et al. Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in 
resting CD4+ T cells. Nat. Med. 9, 727–728 (2003). 
25. 
Fletcher, C. V et al. Persistent HIV-1 replication is associated with lower antiretroviral drug concentrations 
in lymphatic tissues. Proc. Natl. Acad. Sci. U. S. A. 111, 2307–2312 (2014). 
26. 
Lorenzo-Redondo, R. et al. Persistent HIV-1 replication maintains the tissue reservoir during therapy. 
Nature 530, 51–56 (2016). 
 
2. THE PRESENT STUDY  
2.1 STUDY POPULATION 
 
2.1.1 Number of subjects  
 
We will enroll a minimum of 30 patients and a maximum of 50 participants (Fiebig stages I – VI) in the 
study to establish a cohort of early treated patients. We aim at including at least 15 people with an 
incomplete Western Blot (Fiebig I->IV) and as a control we will also include patients with complete 
Western Blot and history of a semi-recent infection (Fiebig V-VI). 
Before sampling, patients willing to participate will be enrolled following informed consent. Study 
participants will be precisely staged at the moment of diagnosis, using the criteria defined by Fiebig et 
al.9 or more up to date serological staging if such becomes available.  
 
2.1.2 Inclusion and exclusion criteria 
 
In order to be eligible, study participants must meet all the following criteria: 
 
• Documented recent HIV-1 infection, early diagnosis.  
- 
clinical symptoms of acute seroconversion and incomplete Western Blot or 
- 
negative screening test within the past 6 months and incomplete Western Blot or  
- 
risk contact within the <3 months and presumable primo-infection with or without clinical 
symptoms and incomplete Western Blot. 
• Able and willing to provide written informed consent  

 
 
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• Age = or >18 years < 65 years 
• Ability to attend the complete schedule of assessments and patient visits for patients 
participating in option A schedule (described below), or ability to attend a partial schedule of 
assessments and patient visits for patients participating in option B (described below).  
• Ability and willingness to have blood and tissue samples collected and stored indefinitely and 
used for various research purposes.  
 
Potential participants meeting any of the following criteria will NOT be enrolled in the study (=exclusion 
criteria): 
 
• Previous or current history of opportunistic infection (AIDS defining events as defined in 
category C of the CDC clinical classification), consisting of chronic HIV-1 infection.  
• Evidence of active HBV infection (Hepatitis B surface antigen positive or HBV viral load 
positive in the past and no evidence of subsequent seroconversion (=HBV antigen or viral 
load negative and positive HBV surface antibody). 
• Evidence of active HCV infection: HCV antibody positive result within 60 days prior to study 
entry with positive HCV viral load or, if the HCV antibody result is negative, a positive HCV 
RNA result within 60 days prior to study entry.  
• Current or known history of cardiomyopathy or significant ischemic or cerebrovascular 
disease. 
• Current history of cancer.  
• Pregnancy or breastfeeding.  
• Any conditions, including psychiatric and psychological disorders, which will in the opinion 
of the investigator interfere with the trial conduct or safety of the participant. 
• Previous participation in a trial evaluating an immune modulating agent  
• Abnormal laboratory tests results at screening:  
1. Confirmed Hemoglobin <11g/dl for women and <12 g:dl for men  
2. Confirmed platelet count < 100000/l  
3. Confirmed neutrophil count <1000/µl  
4. Confirmed AST and/or ALT > 3xULN  
• Active drug or alcohol use or dependence that, in the opinion of the site investigator, would 
interfere with adherence to study requirements. 
• Acute or serious illness, in the opinion of the site investigator, requiring systemic treatment 
and/or hospitalization within 60 days prior to entry. 
 
Patients will be staged according to Fiebig et al. (2003)9. Figure 1 (above) gives a schematic view of the 
Fiebig stages. Standard laboratory tests will be performed to assure accurate staging. Accurate staging 
is part of standard of care in the situation of aute seroconversion.  
2.1.3 Participation Options 
We foresee 2 options to participate in the study. 
Option A:  
Prospective, when the diagnosis was made very recently, the patient will be eligible for option A.  
Option B:  
The patient prefers not to participate in the first in depths sampling, but is willing to participate in a 
selected number of sample collections during follow up as specified in the IC (option B1) or the patient 
decides to participate during a later phase, because the patient already started treatment during acute 
seroconversion in the past (option B2) 

 
 
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TIMEPOINT 
OPTION A 
= patient agrees to the complete deep sampling program 
OPTION B 1/ 2 
= patient agrees to a subset of sampling 
Day 0 
- Peripheral venous puncture 12 x 9 mL  
- Urine sampling 
- Stool sampling 
- Lumbar puncture 
- Inguinal LN resection 
- Left colonoscopy + biopsy  
Patient can prospectively (B1) or 
retrospectively 
(B2) 
decide 
to 
participate in a part of the proposed 
sampling in option A.  
At undetectable VL 
(UVL) 
- Leukapheresis 
- Lumbar puncture 
- Urine sampling 
- Stool sampling 
- Sperm/cervico-vaginal sampling 
Patient can prospectively (B1) or 
retrospectively 
(B2) 
decide 
to 
participate in a part of the proposed 
sampling in option A. 
At 1 year after UVL 
- Leukapheresis 
- Lumbar puncture 
- Urine sampling 
- Stool sampling 
- Sperm/cervico-vaginal sampling 
- Inguinal LN resection 
- Left colonoscopy + biopsy 
Patient can prospectively (B1) or 
retrospectively 
(B2) 
decide 
to 
participate in a part of the proposed 
sampling in option A. 
Month 1 – 24 after 
start of treatment 
at M1, M3, M6, 
M12, M18, M24 
Additional 3 x 9mL blood collection as part of 
a routine blood draw.  
A minimum of 2 additional blood 
draws/ year.  
 
 
2.2 STUDY DESIGN AND INTERVENTION 
 
This is a single arm multicentric non-randomized (prospective) study.  
Note: a consortium agreement is being prepared to extend the project to a multicentre study.  
 
2.2.1 Primary objectives and outcomes 
 
Immunological parameters:  
• Immunoassays to measure human pro-inflammatory mediators. 
• Immunoassays to measure mediators of immune resolution. 
• Assays to measure markers of microbial translocation. 
• Flow cytometric assays to assess phenotype (activation and exhaustion) of innate immune 
cells: monocytes, dendritic cells (DC), natural killer (NK) cells, granulocytes and adaptive 
immune cells: T cells and B cells. 
• Flow cytometric assays to assess function of immune cells, such as antigen uptake and 
phagocytosis, chemotaxis, oxidative burst, cytotoxicity and cytokine secretion, production of 
pro-inflammatory and stimulatory/inhibitory factors, viral inhibition capacity. 
• Analysis of infiltrating immune cells in tissues. 
• Biomarker evaluation on a cellular (multiparameter flow cytometry) and plasma (HIV antigen, 
antibody affinity for antigen, antibody affinity to Fc receptors, antibody subclassing and antibody 
glycosylation) level. 
 
Gene expression analysis/transcriptomics 

 
 
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• Full transcriptome analysis (RNA seqencing) of human genes associated with immunity from 
blood and tissue material. 
• RNA sequencing (RNAseq) analysis of various immune cells and cells expressing cell-associated 
viral RNA (CA RNA). 
• Transcriptome analysis to map micro RNA (miRNA) and long non coding RNA (lncRNAs) 
 
Therapeutic drug monitoring 
• When on stabile cART, TDM (therapeutic drug monitoring) studies to look at cART penetration 
in peripheral tissues. 
 
Microbiome 
• Compositional analysis of gut microbiota in the lower intestinal tract. 
 
Virological parameters 
• Quantification of viral markers as total HIV DNA, integrated HIV DNA, episomal DNA (2LTR 
circles) and cell-associated RNA in different anatomical reservoirs and different cell subsets.  
• Integrations sites sequencing of the region of the human genome where the virus integrates to 
look for clonal expansion.  
• Methylation profiles in the human genome where HIV-1 integrates. 
• Stimulation and inhibition assays to characterise the replication competent viral reservoir 
• Single genome sequencing/ full-length sequencing of proviral HIV 
• Exosomes analysis to determine whether HIV co-factors are present in exosomes and play a 
role in infection 
 
2.2.2 Procedures 
 
2.2.2.1 Eligibility screening and inclusion in the study 
Study participants will be selected from patients already in follow up (for option B) or patients starting 
follow-up at UZ Gent (option A or B). External laboratories will be informed if a positive screening result 
with incomplete Western Blot by the Aids reference lab. They will get information about the possibilities 
for the patient to participate in the study. If samples, send from external labs, hospitals or through the 
general practitioner from high risk groups give a positive screening result with an incomplete confirmation, 
the applicant will be notified immediately to refer the patient as soon as possible to an Aids reference 
center. Screening evaluation will be performed prior to study entry. The patient will be invited to participate 
in the trial and provided information about the aims and risks of the project. After obtaining written informed 
consent, clinical eligibility will be assessed. Patients will be eligible for enrolment if they fulfil all the 
inclusion criteria. Patients will not be eligible for the study if they meet any of the above described 
exclusion criteria. Patients that are already in a follow up and that fulfil the inclusion criteria will be 
proposed to participate starting from a later time point.  
 
The following will be assessed at this visit:  
• Assessment of subject eligibility according to the inclusion and exclusion criteria  
• Demographic and epidemiological data  
• Medical history (past and current), including possible timing of primary HIV infection   
• Physical examination including vital parameters, height and weight  

 
 
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• HIV viral load and CD4 T cell count 
• Laboratory test (non-fasting): hemoglobin, absolute neutrophil count (ANC), platelets, 
creatinine, electrolytes, liver enzymes AST & ALT, coagulation.  
• Hematology- leukocytes, WBC differentiation. 
• Lymphocyte typing- B and T lymphocytes, T helper/suppressor cells. 
• Plasma/serum levels of D-dimer, CRP, complement C3, complement C4.  
• Hepatitis HCV & HBV serology if necessary.  
• Pregnancy test among women. 
• ECG and lung X-ray if required for pre-operative assessment related to the study procedure.  
• Assessment of good peripheral venous access for leukapheresis. 
 
2.2.2.2  In depth sampling OPTION A 
Day 0: first visit to the clinic after positive screening test for HIV-1: study protocol is explained; eligible 
subjects are invited to participate. If patients are willing to participate, they are invited to start the study 
protocol as described below (option A). If not, standard routine clinical care is continued (option B is still 
possible). 
An in-depth sampling will be planned before therapy initiation. Together with our collaborators we will put 
in place a standardised trajectory, aiming for the highest possible comfort for the participants. The patients 
will therefore be admitted in the hospital for 1 day. This will be planned as soon as possible after the first 
contact and HIV-1 diagnosis. This will allow us to start treatment immediately after without any delay. The 
lymph node resection will take place under short general anaesthesia, for the comfort of the patient.  
• Within 24 to maximum 84 hours patients that are included in the study and willing to participate 
are admitted to the hospital for following procedures: peripheral blood sampling (approx. 100 ml 
or 12 x 9 ml), CSF puncture, left colonoscopy, inguinal lymph node excision and stool collection. 
These investigations are part of the study protocol and will be only done in patients that are 
willing to participate and sign the informed consent form.  
• After these investigations, treatment is started immediately based on a quadruple regimen with 
an INSTI, boosted PI and 2 NNRTI’s as the guidelines recommend. The start of cART is part of 
routine clinical care as guidelines recommend early treatment initiation.   
• Follow-up visits are arranged at our aids reference clinic at 1 week post-intervention, 1 month 
(M1), 3 months (M3) and 6 months (M6). The 1 week post-intervention visit is an additional 
study visit. The other visits are part of routine clinical care.  
• At viral load <20 copies/ml, a leukapheresis, lumbar puncture and stool collection is planned. 
These investigations are part of the study protocol.  
• One year after the first visit, a second in depth sampling is planned, as part of the study protocol: 
repeating colonoscopy, lymph node excision, lumbar puncture, semen, urine and stool sampling 
and leukapheresis. The lymph node resection at this stage will again take place under short 
general anaesthesia. The colonoscopy can take place under sedation or under the same general 
anaesthesia, depending on the patient request for general anaesthesia. 
• At every standard blood drawing for routine follow-up an extra 3 tubes of blood of approx. 30 
ml will go the lab for analyses following the study protocol.  
 
PART of routine clinical care:  

 
 
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• Intake visit Day 0 at positive screening in the aids reference center.  
• General lab analysis with confirmation test, viral load, blood count and CD4 count, co-infection 
screening and biochemistry. 
• Start of cART early after diagnosis.  
• Follow-up at M1, M3 and M6: clinical and biochemical follow-up.  
 
PART of the study protocol:  
• Explanation of the study protocol at the intake visit D0 and if willing to participate signing of ICF 
and planning of additional investigations.  
• Sampling before treatment initiation: blood sampling, CSF puncture, left colonoscopy and inguinal 
lymph node excision.  
• 1 week post-intervention: clinical control as part of the study visit.  
• Extra blood drawing at routine blood analysis at M1, M3, M6, M12, M18 and M24. 
• Sampling at reaching undetectable viral load: stool, urine and genital sampling, leucapheresis 
and CSF puncture. 
• Sampling one year after reaching undetectable viral load: stool, urine, genital and blood sampling, 
CSF puncture, left colonoscopy and inguinal lymph node excision.  
 
If one of these invasive procedures would reveal any abnormalities, unknown to the patients and his 
physician, diagnostics and therapeutics will be effectuated as to be expected in these cases (ex biopsy, 
exeresis of a suspect lesion). Follow-up of these results will be foreseen by the treating physician of the 
patient.  
 
Note: the sampling can be adapted based on individual characteristics of the patients. If patients are not 
willing to have one of the procedures or there is a contra-indication, this part will be left out. We aim to 
include at least 30 of our patients for the entire study protocol and all the procedures it involves.  
 
2.2.2.3 In depth sampling OPTION B 
Patients that decide not to start the study protocol can still decide to participate in the later phase. This 
option B group can be divided in 2 subgroups: 
• B1: The group of patients that decide prospectively not to participate in the first in depths 
sampling, but is willing to participate in a selected number of sample collections during follow up 
as specified in the IC. 
• B2: The group of patients that participated as part of the early seroconverter cohort in the study 
(Reference number: EC 2013/468) or that started treatment early during acute seroconversion 
over the last 4 years and are interested to participate starting from a later time point and in a 
selected number of sample collections during follow up as specified in the IC. 
 
2.2.2.4 Sampling will consist of:  
 
Leukapheresis 
Participants will undergo leukapheresis at the Ghent University Hospital. Leukapheresis runs will last 
approximately three hours for the collection of > 1x108 cells Peripheral Blood Mononucleair Cells 

 
 
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(PBMCs). Leukapheresis is considered the gold-standard method for obtaining large volumes of 
peripheral cells from HIV-infected patients, and has been performed safely in individuals with and 
without hematologic malignancy and/or HSCT (1). Leukapheresis will be performed twice for each 
participant, with a one year interval following the initial collection. If contra-indicated this procedure will 
be replaced by a peripheral blood draw of 12x9ml. The first leucapheresis will be performed once 
undetectable viral load is reached, the second leucapheresis will be performed one year after the first 
leacapheresis time point (max interval 16 months).  
Lymph node resection 
The vascular surgery department will perform lymph node resection. Briefly, a small incision is made in 
the inguinal region (triangle of scarpa) allowing a lymph node resection. Lymph node resection will be 
performed twice, before cART is initiated and after one year of chronic treatment after undetectable viral 
load.   
 Colonoscopy 
We will perform collection of gut-associated lymphoid tissue (GALT) via biopsy of rectal mucosa. Rectal 
mucosal sampling will be obtained by sigmoidoscopy, collecting up to 10 mucosal biopsies. If patients 
agree the second phase of the sampling will consist of a full length colonoscopy with biopsies taken at 
the terminal ileum and colon.  
Subjects will be counselled to avoid rectal trauma and the use of anticoagulants (e.g. aspirin, NSAIDS) 
before and after the procedure. Mucosal biopsies will not be taken if the participant has an increased risk 
for complications, including receptive anal intercourse within 3 days of the procedure, an active anal 
infection, or recent use of anticoagulants. Gastroenterologists who have training and clinical certification 
in sigmoidoscopy and rectal mucosal biopsy will perform rectal biopsies. This procedure will be performed 
twice for each participant.  The sigmoidoscopy will be performed before cART is initiated, the (second) 
full length colonoscopy will be performed one year after reaching an undetectable viral load during chronic 
treatment. 
Lumbar puncture  
Cerebrospinal fluid (CSF) will be obtained for study purposes and processed in standardized fashion as 
previously described in the study of central nervous system HIV-1 infection (2). A maximum volume of 
3-5 ml will be collected. Patients, currently on systemic anticoagulation (e.g. warfarin therapy), with a 
platelet count < 50,000 per uL or with clinical signs of systemic infection won’t be included. Prior to 
lumbar puncture, a certified physician and study co-investigator will perform a cranial nerve exam; 
lumbar puncture will not be performed if evidence of intracranial pressure is identified. This procedure 
will be performed three times for each participant: before cART is initiated, at the time of reaching 
undetectable viral load and one year after reaching an undetectable viral load during chronic treatment.  
Genital tract access 
Sperm will be collected according to the standard operating procedures from our fertility department. 
Cervicovaginal secretions will be harvest as described by Zara et al. (3). This procedure will be 
performed twice for each participant: at the time of reaching undetectable viral load  and one year after 
reaching an undetectable viral load during chronic treatment.g. Urine sample 

 
 
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14 
A mid-stream urine sample will be collected. This means that you don’t collect the first or last part of 
urine that comes out. This reduces the risk of the sample being contaminated with bacteria. Urine will be 
collected in a sterile container and stored in the fridge immediately (room: 120 040). We will collect urine 
at two time points at the time of reaching undetectable viral load  and and one year after reaching an 
undetectable viral load during chronic treatment. 
References:  
1. 
Molina A et al. Blood reviews (2003); 17: 249 
2. 
Price RW et al. Aids (2001); 15: 125 
3.           Zara F et al. Sexually transmitted infections (2004); 80: 108 
 
2.2.3 Flowchart  
 
 
 
 
 
 
 
 
 
Figure 2: Sampling schedule. LN = lymph node. LP = lumbar puncture. WB = western blot. VL = viral load. Stars 
represent blood draws at 6, 12, 24, 36, 48 and 60 weeks post infection 
2.3 DESCRIPTION OF THE LABORATORY RESEARCH TECHNIQUES 
2.3.1 Immunological analysis  
• Immunoassays to measure human pro-inflammatory mediators and markers of microbial 
translocation using ELISA or Luminex: 
IL-1α, IL-1β, IL-6, IL-7, IL-17a, TNF-α, IFN- γ, myeloperoxidase, neutrophil elastase, cathepsin 
G, neutrophil defensins, nitric oxide, reactive oxygen species, I-FABP, sST2, zonulin-1, EndoCab 
IgM, LBP, sCD14, KT ratio and others 
 
• Immunoassay to measure the inflammation marker CRP by immunoturbidimetric assay 
 
• Immunoassays to measure mediators of immune resolution using mass spectrometry: 
 
lipoxins, resolvins, maresins, protectins 
 
• Flow cytometric assays to assess phenotype of innate immune cells: monocytes, dendritic cells 
(DC), natural killer (NK) cells, granulocytes and adaptive immune cells: T cells and B cells 

 
 
Protocol, version I, dd. 25/01/2018 
15 
o 
Lineage markers: CD45 (leukocyte common antigen), CD3, CD4, CD8, CD45RA, CD45RO 
(T cell lineages markers), CD19 (B cell), CD56, NKG2A/NKG2C, 2-domain and 3-domain 
KIR (NK cell), CD66b (neutrophil), CD68 and CD33 (macrophage), CD14 (monocyte), 
CD11c (mDC), CD123 (pDC)  
o 
Activation markers: CD69, CD38, HLA-DR, CD62L, CD16, CD25 
o 
Cell proliferation marker: Ki67  
o 
Terminal differentiation and proliferative history marker: CD57  
o 
DC maturation markers: CD80, CD83, CD86 
o 
Immune exhaustion (Plasma markers: D-dimer, soluble CD163, soluble CD14, IP-10, IL-
6 ; HIV-specific T cell: PD-1, LAG-3, Tim3 expression) 
 
• Flow cytometric assays to assess function of immune cells 
o 
Phagocytosis (neutrophils, monocytes, dendritic cells) 
o 
Chemotaxis (neutrophils, monocytes) 
o 
Oxidative burst (neutrophils, monocytes) 
o 
Cytotoxicity and cytokine secretion (NK and T cells) 
o 
Immune signalling (secretion of cytokines, chemokines, immune-stimulatory or immune-
inhibitory factors upon in vitro cell stimulation) 
o 
Viral inhibition assay (VIA) will be performed to measure the ability of NK and CD8 T cells 
to inhibit HIV-1 replication. In brief, sorted NK cells or CD8 T cells are incubated with HIV-
1-infected autologous CD4 T cells. At predetermined time points, supernatant will be 
collected and the amount of HIV-1 will be quantified using p24 ELISA. 
 
• Infiltrating innate immune cells and lymphoid tissue fibrosis on formalin fixed tissue samples 
To be able to quantify the number of infiltrating innate immune cells, fixed tissue sections 
will be stained. We will evaluate the infiltration of neutrophils (anti-human (αh) neutrophil 
defensins), macrophages (αhCD68, αhCD33), dendritic cells (DC) [αhDC11c (BDCA-1), 
αhCD123 (BDCA-2)], natural killer (NK) cells (αhCD56, αhNKp46) and T cells (αhCD8 and 
αhCD4). 
• Biomarker evaluation on a cellular (multiparameter flow cytometry) and plasma level (HIV 
antigen, antibody affinity for antigen, antibody affinity to Fc receptors, antibody subclasses and 
antibody glycosylation). 
o PBMCs will be stained for cell associated RNA, isolated by fluorescent activated cell sorting 
(FACS) and subjected to RNA seq analysis to identify markers of latency. The identified 
markers will be validated by multiparameter flow cytometry and examined in the relation to 
previously identified cellular markers of latency. 
o Plasma samples will be used to assess the affinity of antibodies to different viral antigens. 
Next, affinity of antibody Fc fragment to Fc receptors (FcRs) will be assessed by Biacore 
(GE Healthcare) or Evalution platform (MyCartis). Additionally, antigen-specific antibody 
subclasses (IgG1, IgG2, IgG3, IgG4, IgA1, IgA2, IgM) will be determined by Luminex 
platform or Evalution (MyCartis) technology. Antibody glycosylation profiles will be 
assessed by labelling glycans with 8-aminopyrene-1,3,6-trisulfonic acid and analysing by 
capillary electrophoresis.  
 
2.3.2. Inflammatory parameters 
We would like to look for biomarkers of axonal injury and neurodegeneration in the cerebrospinal fluid. 
We will closely collaborate with Prof Magnus Gisslen, University of Gothenburg and expert in the field, 

 
 
Protocol, version I, dd. 25/01/2018 
16 
doing additional testing of CSF measuring inflammatory parameters like neurofilament protein light, 
neopterin and CSF/plasma albumin ratio (8). Other markers of immune activation in blood and/or CSF 
can also be assessed for example IL-6, TNF-alpha, HLADR+CD38+, CD14s, CRP and 
beta2microglubuline.  
 
2.3.3. Gene expression analysis/transcriptomics 
  
• Transcriptome analyses with the use of quantitative PCR (qPCR) or RNA sequencing (RNAseq) 
technology will be used to explore expression profiles of genes associated with immunity. Sorted 
immune cells or cells excised by laser capture microdissection from fixed/frozen tissue specimens 
will be subjected to RNAseq technology. Single RNAseq data analysis pipelines will be used (i.e. 
SINCERA) and ready to be implemented for determining cell type specific gene signatures. This 
includes quality control (i.e. FASTQC), read mapping (i.e. Tophat), cell type identification and 
signature & driving force analysis (i.e. SINCERA). Total RNAseq will be performed on Illumina 
Hiseq 2500 with 10-100 ng input of ribodepleted RNA per patient. Data analysis will involve quality 
control, mapping of the reads (Tophat) and gene quantification together with differential 
expression analysis (edgeR). Next, Ingenuity Pathway analysis (IPA) will allow performing gene 
set enrichment analysis and gene ontology. 
• The expression profile of specific RNA factors related to immunity or potentially playing a role in 
HIV replication will be determined by qPCR (restriction factor analysis).  Technology as described 
above. 
• RNAseq analysis of cells expressing cell-associated RNA (CA RNA) will be used to explore the 
changes in gene expression of infected cells. Technology as described above. 
• Transcriptome analysis to map micro RNA (miRNA) and long non coding RNA (lncRNAs). 
Technology as described above. The non-coding (nc)RNAs are known to control and direct 
transcriptional and posttranscriptional processes in, offering unique possibilities for pathogens 
to hijack the cellular machinery and reshape gene expression in their favor. Therefore, studying 
transcriptome changes upon viral infection with a focus on ncRNAs will be crucial to elucidate 
the pathways of viral persistence. These expression datasets will be overlapped to investigate 
broad viral response mechanisms as well as virus- specific changes to the host transcriptome. 
Transcription factor analysis will be included to investigate how the transcriptome changes can 
be explained. Functional validation will focus on ncRNAs as these molecules are shown to be 
crucial for viral persistence.  
 
2.3.4. Therapeutic drug monitoring (TDM) 
To estimate the viral reservoir in the different anatomical compartments, the determination of the local 
concentrations of the administered drugs is of great importance. Sufficient knowledge on drug penetration 
in peripheral tissues of the current therapies in use is missing. Some studies show that due to lower 
concentration of certain antiretrovirals in lymph nodes, persistent viral replication occurs7. This source of 
continuous viral replication could be the in vivo origin of relapsing virus at treatment interruption. To 
determine treatment concentrations, we will work in collaboration with Prof. A. Verstraete and different 
techniques as tandem mass spectrometry and ultra performance liquid chromatography will be used.  
2.3.5. Microbiome monitoring 
 

 
 
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Stool microbiome will be analysed using next-generation sequencing (NGS) of 16S rRNA gene amplicons 
to identify bacteria at genus/species level and assess the corresponding gut enterotype. 
 
2.3.6. Virological analysis 
• Cell sorting of the different cell populations.  
To investigate the viral reservoir in different cell subsets, we will isolate immune cells from the 
collected biopsies and sort different cellular subsets (methods for cell isolation and sorting have 
been optimised in our lab for the HIV STAR study), if the amount of immune cells recovered allows 
for further differentiation.  
PBMCs will be isolated from peripheral blood samples by density gradient centrifugation. CD4 
isolation will be performed by magnetic beads (negative selection). Cell subsets will be isolated 
by flow cytometry cell sorting, using antibody labelling based on cell surface markers. From the 
blood compartment we will isolate CD8 T cells (CD45+CD3+CD8+), monocytes (CD45+CD14+), 
NK cells (CD45+CD56+CD16+) and B cells (CD45+CD19+). From the pre-sorted CD4 T cell 
fraction, we will further differentiate Tcm-Tem, Ttm and naïve T cells based on the expression of 
CD45RO, CD45RA, CD27 and CCR7.  
A fraction of the lymph node biopsy and 2 colon biopsies will be stored for further 
immunohistochemical analysis. Colon samples will be treated using an optimised protocol for cell 
isolation, after which CD45+ immune cells will be isolated using fluorescence activated cell sorting 
(FACS). Cells extracted from the lymph node will be pre-sorted by CD4 negative selection and 
sorted based on the Tcm-Tem phenotype (cfr above markers). 
• Quantitative assessment of the HIV-1 viral reservoir in the plasma and in different cellular 
fractions of the different anatomical sites. 
Our data have shown that HIV-1 is present in 
different anatomical compartments throughout 
the body1. Sorted cell populations from the 
different tissues will be evaluated using a set of 
viral reservoir assays based on HIV-1 RNA/DNA 
intermediates. These assays have been 
translated by our group from in vitro research 
towards the clinic, using state of the art droplet 
digital (dd) PCR technology, which allows 
absolute ultrasensitive quantification of viral 
DNA and RNA. The cellular fractions from blood  
and the anatomical compartments will be 
separated and subjected to  quantification of 
total HIV-1 DNA, 2LTR (long terminal repeat) 
circular HIV-1 DNA, integrated HIV-1 DNA 
and cell-associated RNA.  
We will perform quantification of  episomal 
HIV-2LTR circles in different anatomical sites to 
detect ongoing viral replication. These 2LTR 
Figure 3: When a cell is infected with HIV-1, 
linear cDNA is formed and moves to the 
nucleus, where it is incorporated into the 
host genome as a provirus. When integration 
was not successful, unintegrated sequences 
recombine at their long terminal repeat 
(LTR), to form 1- or 2-LTR circles. Figure: 
Schacker34 

 
 
Protocol, version I, dd. 25/01/2018 
18 
circles have been recognised as a marker of ongoing replication. 2LTR quantification assays 
have been translated from in vitro to in vivo settings, mainly in PBMCs2. Our current data show 
high levels of 2LTRs in PBMCs of recent seroconverters.  
Integrated HIV-1 DNA is a marker for the amount of infected cells and will be quantified using 
the Alu-HIV PCR method, as described by De Spiegelaere et al.  This technique relies on the use 
of a nested PCR, where a specific human repeat element, the Alu element, is recognised by the 
first primer. The second primer of the first PCR recognises an HIV sequence.3  
Full-length cell associated RNA forms a marker for HIV-1 DNA transcription and has been 
used in the context of clinical trials aiming at activating the latent reservoir4. We have adapted 
these assays towards a clinical user-friendly ddPCR platform5.  
• HIV-1 integration site analyses of the viral reservoir in different anatomical sites:  
Integration site analysis will be performed to identify if the replication competent viral reservoir 
mainly clonally expanded (indicating homeostatic proliferation as mechanism for viral 
persistence. CD4+ T cell populations, sorted from the different tissues will be evaluated using 
LAM-PCR/nrLAM-PCR and deep sequencing6. The LAM-PCR strategy uses a linear 
amplification by PCR with an outward-bound HIV-1 specific primer. These linear amplicons 
containing part of the human genome sequence of the integration site are subsequently 
analyzed by deep sequencing. Our strategy is based on a combination of target capture (TC) 
sample enrichment and next-generation sequencing. Our preliminary data shows integrated 
HIV-1 genome over all the chromosomes. We are currently evaluating the presence of unique 
integration sites. This project will constitute the first study to evaluate integration sites in 
anatomical compartment to map HIV-1 integration in vivo. We have recently optimized an assay 
to identify HIV-1 integration site in the patient genome. Our assay has been validated both on 
HIV-1 infected cells and patient-derived samples. We analysed HIV-1 infected patient-derived 
samples before treatment and analysed the integration site pattern.  
• Analysis of the HIV-1 methylome in different anatomical sites:  
The HIV-1 methylome of proviral HIV-1 DNA will be assessed by bisulphite conversion and 
deep sequencing using an Illumina platform. Extracted DNA will be bisulphite treated to 
substitute all unmethylated Cytosines into Uracyls. Subsequently, a targeted PCR for the sense 
and antisense (as a control of the native sequence) strand will be performed to specifically 
isolate the HIV-1 CpG islands. Finally, methylation profiles are assessed by deep sequencing, 
enabling the analysis of separate HIV-1 DNA molecules within one sample. 
• Exosomes: 
As exosomes are excreted from typical reservoir cells such as CD4+ T cells, one can hypothesize 
that viral DNA or other viral markers are present in these exosomes even under full suppression 
of the virus and therefore can serve as future markers for HIV-1 latency in patients. The presence 
of co-factors in exosomes and/or differential compositions will be verified in exosomes obtained 
from blood samples of HIV-1 infected patients. For exosome proteomics, we will use a Stable 
Isotope Labeling by Amino acids in Cell culture (SILAC) approach. The principle of SILAC labeling 
is based on metabolic incorporation of given non-radioactive isotopic forms of an amino acid in 
the culture media into cellular proteins. Typically, SILAC experiments start with two cell 

 
 
Protocol, version I, dd. 25/01/2018 
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populations: one is labeled in the culture medium composed of heavy isotopic 13C6 L-lysine and/or 
13C615N4 L-arginine for 6 doublings, while the other is maintained in the same medium but with 
normal L-lysine and/or L-arginine for the same period. Proteins are extracted from the two cellular 
populations respectively, 1:1 mixed and subjected to mass spectrometry. The relative intensities 
of mass spectrometric peak(s) generated from a protein reflect its relative abundance. A complete 
analysis of bioactive molecules packaged in the exosomes will be performed including: 
o Identification of specific cellular markers of latently infected cells by proteome analysis 
o Identification of viral proteins packaged in exosomes through mass spectrometry 
o identification of viral RNA species by standardized RT-PCR techniques 
o identification of cellular RNA (specific miRNA) 
o identification of viral DNA through ligation-mediated PCR and subsequent Illumina 
sequencing 
o comparison of exosomes from latently infected cells before and after reactivation with 
Latency Reversing Agents (LRAs) 
 
• Stimulation and immunological inhibition assays: VOA (Viral Outgrowth Assay)/TILDA (Tat/rev 
Induced Limiting Dilution Assay).   
o Infectious units per million cells- IUPM: The principal approach for quantifying HIV-1 
persistence during antiretroviral treatment (ART) is a viral outgrowth assay (VOA) 
performed on resting CD4 T cells. These cells do not produce virus without stimulation. 
Therefore, resting CD4 T cells are stimulated with phytohemagglutinin (PHA) in the 
presence of irradiated allogeneic peripheral blood mononuclear cells. These stimuli induce 
global T cell activation, which reverses latency at least in a fraction of cells carrying 
integrated HIV-1 genomes. The viruses released from these cells are expanded in 
MOLT4/CCR5 cell line and detected after 2 weeks in the supernatant. The frequency of 
latently infected cells, expressed in terms of infectious units per million (IUPM) resting CD4 
T cells. In principle, this assay can also detect resting CD4+ T cells harbouring labile 
unintegrated forms of HIV-1 DNA, although the frequency of cells containing unintegrated 
DNA during ART is low. Positive wells at each dilution were counted and the maximum 
likelihood method was used to calculate the frequency of cells with inducible replication 
competent HIV-1 (http://bioinf.wehi.edu.au/software/elda). 
o Tat/rev Induced Limiting Dilution Assay – TILDA: Enriched CD4+ T cells are re-suspended 
at 2 x~ 106 cells/ml in media and rested for 3–5 h at 37 °C, 5% CO2. CD4+ T cells are 
stimulated for 12 h with 100 ng/ml PMA and 1 µg/ml ionomycin (both from Sigma). The 
duration of 12 h was based on kinetic experiments demonstrating maximal production of 
tat/rev RNA and preserved cell viability at this time point. After stimulation, cells are serially 
diluted to 18 x~ 106 cells/ml, 9 x~ 106 cells/ml, 3 x~ 106 cells/ml and 1 x~ 106 cells/ml in 
culture medium. 
The cell suspension from each serial dilution is distributed in 22 to 24 wells of a 96 well 
plate corresponding to 18,000, 9000, 3000 and 1000 cells per well. Pre-amplification was 
carried out. At the end of the pre-amplification, TE buffer was added to each well and the 
diluted PCR products were used as template for the tat/rev real-time PCR reaction (normal 

 
 
Protocol, version I, dd. 25/01/2018 
20 
PCR). This reaction was performed using a real time PCR (Light Cycler 480, Roche Life 
Science). Positive wells at each dilution were counted and the maximum likelihood method 
was used to calculate the frequency of cells with inducible HIV msRNA. 
(http://bioinf.wehi.edu.au/software/elda). 
 
• Single genome sequencing/ full-length sequencing of proviral HIV 
Full-length genome sequencing of proviral HIV will be performed by nested PCR with Illumina 
MiSeq. This strategy enables to quantify the relative proportion of sequence-intact viruses in the 
sorted cell populations. DNA amplicon sequences will be aligned with an HXB2 reference and 
jModeltest v0.1.1 will be used to infer the best phylogenetic model to explain the alignment 
sequence evolution. Identification of hypermutated sequences will be performed using hypermut 
2.0. Stop codons, sequence inversions and deletions in viral open reading frames will be 
identified using automated sequence analysis approaches, using standard software. 
Biosafety:  All screening tests on patient material, isolation and sorting will be done in L2 
facilities. Stimulation and culture of prelevated cells will be effectuated in an L3 facility.  
 
References 
1. Ananworanich, J., Dubé, K. & Chomont, N. How does the timing of antiretroviral therapy initiation in acute 
2. infection affect HIV reservoirs? Curr. Opin. HIV AIDS 10, 18–28 (2015). 
3. Malatinkova, E. et al. Accurate quantification of episomal HIV-1 two-long terminal repeat circles by use of 
optimized DNA isolation and droplet digital PCR. J. Clin. Microbiol. 53, 699–701 (2015). 
4. De Spiegelaere, W. et al. Quantification of integrated HIV DNA by repetitive-sampling Alu-HIV PCR on the 
basis of poisson statistics. Clin. Chem. 60, 886–895 (2014). 
5. Rasmussen, T. A., Tolstrup, M., Winckelmann, A., Østergaard, L. & Søgaard, O. S. Eliminating the latent HIV 
reservoir by reactivation strategies: Advancing to clinical trials. Hum. Vaccines Immunother. 9, 790–799 (2013). 
6. Kiselinova, M. et al. Comparison of droplet digital PCR and seminested real-time PCR for quantification of cell-
associated HIV-1 RNA. PLoS One 9, 1–8 (2014). 
7. Schmidt M et al. Nature methods (2007); 4: 1051  
8. Fletcher CV et al. Proceedings of the National Academy of Sciences of the United States of America 
2014,111:2307-2312. 
9. Jan Jessen Krut et al., Plos One (2014) e88591 
 
3. RISKS AND ADVANTAGES 
 
3.1 RISKS  
In this project proposal, we have two important (risk related) ethical questions:  
3.1.1 Risks related to patient sampling 
For all individual procedures, the individual risk will be discussed with the patient by an open 
communication. For each procedure, the reported individual risks are low (typically 1/1000 for adverse 
events in all procedures), and are based on data from sick patients (e.g. lung disease for which 
bronchoscopy is needed). Also the patient's cumulative risk (all procedures taken together) will be 
discussed extensively. Risk estimation per procedure is shown below. 

 
 
Protocol, version I, dd. 25/01/2018 
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Lumbar Puncture (LP) 
Possible complications comprise of local discomfort with pain at the puncture site, during or after the 
puncture, radicular pain, bleeding, infection and post-puncture headache. A recent review (Wright et al J 
Neurol 2012; 259:. 1530-45) reported  infections and bleeding, and each was seen in less than 0.01% of 
the cases. The incidence of post-puncture headache (PPH) is a fairly frequent complication and its 
incidence is highly dependent on the needle used. If an atraumatic needle is used, PPH is reported on 
average in 3-9% of the cases (Wright et al J Neurol 2012; 259:. 1530-45; Lavi et al Neurology 2006; 67; 
1492-1494.). All the punctures within this study will be made with an atraumatic needle. Researchers 
investigated the prevention of PPH in an observational study with cross-sectional data analysis 
(Monteiro de Almeida et al Headache 2011; 51:. 1503-10). Total of 675 LPs were performed involving 
477 volunteers (575 puncture in HIV-positive individuals and 100 in healthy volunteers). PPH was noted 
in only 0.9% of the subjects. Most cases of PPH (92%) recovered spontaneously or with medication. 
Three individuals were treated by an epidural blood patch. In UZ Gent an epidural blood patch is used 
with a protocol performed by an anaesthesiologist with specific expertise. 
Biopsy of the gastrointestinal tract 
A colonoscopy with biopsy carries a risk of bowel perforation in 1/1500. If this occurs, the perforation is 
recognised immediately and treated during the same endoscopy. As a result of the administration of 
analgesics and/or narcotic drugs other side effects can occur, such as low blood pressure, nausea, or 
twists. These are short-lived side effects and after a colonoscopy, the patient is kept in observation 
overnight, with monitoring of the pulse and blood pressure. Subjects will be counselled to avoid rectal 
trauma and the use of anticoagulants (e.g. aspirin, NSAIDS) before and after the procedure. Mucosal 
biopsies will not be taken if the participant has an increased risk for complications, including receptive 
anal intercourse within 3 days of the procedure, an active anal infection, or recent use of anticoagulants. 
Biopsies will be performed by gastroenterologists who have training and clinical certification in 
coloscopy/ anoscopy.  
Biopsy of the lymph node 
Lymfocele is the main risk in removal of lymph nodes. This complication is infrequent (<1%) and can be 
surgically corrected. The infectious risk is <1% and easily treatable. 
Leukapheresis 
This is considered a safe procedure. All studies available were done in patients with hematologic or solid 
tumours malignancies (ex. Reik, 1997). The most frequent side effect (39%) was paresthesia due to 
citrate-related hypocalcaemia (1 in 10). This could easily be managed with oral calcium supplements and/ 
or slower flow rates. Other reactions included hypotension (4%) and headache (1,4%). Patients under 
antihypertensive treatment, will be asked to interrupt this treatment the day of the procedure. The bleeding 
risk after the procedure is transitory increased. There is also risk of catheter problems during procedure. 
Leukapheresis will not take place if screening beforehand reveals poor peripheral venous access or 
electrolyte disturbances. In these cases, the procedure will be replaced by a peripheral blood puncture 
(6x9ml).  
Semen sample, vaginal lavage and urine sampling 
These are non-invasive procedures and not associated with serious adverse effects.  

 
 
Protocol, version I, dd. 25/01/2018 
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Anaesthesia 
Lymph node excision is done under short general anaesthesia in most cases, because of better 
tolerability and comfort for the patient. Most healthy people don't have any problems with general 
anaesthesia. Although many people may have mild, temporary symptoms, general anaesthesia itself is 
exceptionally safe, even for the sickest patients. The risk of long-term complications, much less death, is 
very small. In general, the risk of complications is more closely related to the type of procedure, the 
general physical health, than to the anaesthesia itself. Some of the factors that can increase the risk of 
complications include: smoking, obstructive sleep apnoea, obesity, high blood pressure, diabetes, other 
medical conditions involving your heart, lungs or kidneys, medications, such as aspirin, that can 
increase bleeding, history of heavy alcohol use, drug allergies and history of adverse reactions to 
anaesthesia. Rare complications, which may occur more frequently in older adults or in people with 
serious medical problems, include: temporary mental confusion, lung infections, stroke, heart attack, 
and death.  
3.1.2 Risk due to the psychological effect of recent HIV diagnosis  
Recent diagnosis makes patients more vulnerable to participate in a study without having balanced very 
well their engagement. In recent studies performed at the HCRC we included both treatment experienced 
but also treatment naïve patients (HIV STAR: 2015/0894, Amfar Study EC 2013 468). In the study that 
included patients with a recent diagnosis, blood sampling and gut biopsies were taken. Patients have a 
strong interest in the scientific results and we evaluated the study design by standardised questionnaires 
and most participants did have a very positive experience. We are continuously optimizing the procedures 
based on this received feedback. In addition, patients will be questioned about their engagement multiple 
times after the first sampling phase. The protocol will be rediscussed with them and they have the 
possibility to end their engagement at any time during the course of the study. Patients that present with 
acute seroconversion are included in the multidisciplinary care path at our AIDS reference centre, where 
they have the possibility to discuss their recent diagnosis and the psycho-social consequences with a 
team of doctors, social nurses and psychologists. We have from previous sampling studies created an 
intern peer reviewing system where we discuss potential issues and cases with Prof. Dr. Dirk Vogelaers.  
3.1.3 Risk of not reaching enough study participants 
This question rises whether this study will find enough motivated participants to participate. Therefore, an 
initial inquiry with several patients (N = 10) has already shown us that patients are indeed motivated to 
engage in such a study, provided that they are adequately informed about the scientific design and gain 
of the experiments. The burden of the intensive lifelong intake of ART medication causes HIV-infected 
patients, more than healthy volunteers, to actively participate in studies that contribute to the search for 
an HIV cure. The clinical studies that we set up are presented at the yearly BREACH (organisation unifying 
all AIDS reference centres in Belgium) congress and the advice of the positive counsel is asked.   
In order to optimise patient inclusion recruitment will be organised in cooperation with the partner 
institutions Institute of Tropical Medicine Antwerp and the University Hospital Brussels.  
3.1.4 Risk of misperception of the study 
An important ethical conundrum lay in the false perception patients may have with regard to this project. 
These “therapeutic misconception and misestimation” are well known concepts in bioethics. Patients that 

 
 
Protocol, version I, dd. 25/01/2018 
23 
participate in this study might perceive the wrong expectations from the study. Although there will be no 
medical intervention (no admission of a study drug), the patient might perceive this study as having an 
impact on his ‘HIV reservoir’. They lead potential participants and/or practitioner to over-consider the very 
theoretical advantage (participating in a Cure diagnostic study) and under-consider the side effects of the 
study. It will be a matter of explaining the study correctly and designing a good balanced informed consent 
that will be readily understandable to the potential participants. 
4. STUDY ANALYSIS  
 
4.1 SAMPLE SIZE CALCULATION 
 
The number of patients (N=50) that we will investigate exceeds by far the numbers reported in previous 
studies on HIV-1 reservoir dynamics, and should provide ample power to reveal differences between 
different patient cohorts and compartments within this specific patient cohort while still adhering to the 
budget constraints.  
4.2 DATA ANALYSIS 
Samples and results will be anonymised by Prof. Dr. Linos Vandekerckhove and Karen Vervisch and 
analysed under supervision of postdoctoral students  Dr. Eva Maltinkova and Dr. Magdalena Sips at HIV 
Cure Research Center.  
4.3 STATISTICAL ANALYSIS 
Patients will be divided into groups depending of Fiebieg stage at the diagnosis. Statistical comparisons 
of various parameters will be performed with the Kruskal-Wallis test. P-values of pairwise comparisons 
will be adjusted using Dunn’s method. Reported P-values will be two-sided and values <0.05 will be 
considered significant. Spearman’s rank correlation coefficient will be used to examine the relationship 
between immunological and virological parameters, such as activation status of innate immune cells and 
the size of HIV DNA viral reservoir seeded early in infection. When appropriate, logarithmic 
transformation of the data will be performed to facilitate normalization of the data distribution and to 
perform parametric tests. Adjustment for multiple testing will be done using Bonferroni correction. 
Statistical analyses will be performed using SPSS or GraphPad Prism programs. 
4.4 STORAGE AND SHIPMENT OF THE SAMPLES 
 
4.4.1 Sample processing 
 
PBMCs will be stored in liquid nitrogen at Bimetra biobank, UZ Gent at -196°C in FCS/DMSO for further 
analysis. PBMC’s will be used for immunological analysis as described on heading 2.3.1 and 2.3.2 of the 
protocol. 
Plasma samples will be stored at -80°C in HIV cure research center lab, room number 120 040; MRBII 
building, second floor and used both for biomarker evaluation (protocol:2.3.1) and virological assays 
(protocol: 2.3.6). 

 
 
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Also DNA will be stored at -20°C, RNA isolates will be stored at -80°C in HIV cure research center lab 
room 120 040. DNA/ RNA will be used for gene expression analysis as described in the protocol 2.3.3. 
and for  virological analysis (protocol: 2.3.6). 
Stool samples will be stored at -80°C in HIV cure research center lab room 120 040 and used for 
micobiome evaluation (protocol:2.3.5). 
Formalin fixed paraffin embedded (FFPE) samples will be stored in HIV cure research center labs room 
120 040 and used both for biomarker evaluation (protocol: 2.3.1) and virological assays (protocol: 2.3.6). 
Analysis of HIV integration sites and HIV methylome (protocol: 2.3.6) are done in collaboration with Lisa 
Frenkel, Seattle Children's Hospital and anonymized samples will be send over to the Frenkel lab for 
analysis. Single HIV genome sequencing and full length HIV sequencing (protocol: 2.3.6)  will be 
performed on RNA/DNA in collaboration with the Mathias Lichterfield lab Lichterfeld at MIT and Harvard, 
Boston, USA and anonymized samples will be send over to the Frenkel lab for analysis.  
Cerebrospinal fluid will be used for biomarkers of axonal injury and neurodegeneration in the 
cerebrospinal fluid. We will closely collaborate with Prof Magnus Gisslen, University of Gothenburg and 
expert in the field, doing additional testing of CSF measuring inflammatory parameters like 
neurofilament in his lab. Therefore cerebal fluid samples will be stored in HIV cure research center labs 
room 120 040 and send over to Gotenburg for analysis. Samples that are not used at the Frenkel, 
Lichterfield and Gisslen lab will return to the Bimetra biobank or will be destroyed. Samples are 
analysed by PhD students of the HIV Cure Research Group of Prof Vandekerckhove that perform a 
research stay in a foreign lab.  
 
As this are very precious samples, samples will be stored at the Bimetra biobank, UZ Gent or at the HIV 
cure research center lab, roomnumber 120 040; MRBII building, second floor for 20 years.  
 
5. DURATION AND TERMINATION OF STUDY 
 
The clinical study (including sampling before therapy initiation, during follow-up) will be performed over a 
timeframe of maximum 2 years. We expect to finish the analysis in 4 years. We hope to include patients 
starting from September 2017 until the 1st of January 2023. Participation in this study is voluntary. Patients 
can refuse to participate or ask to end the participation before the final closure of the study, at any time. 
Patients themselves can be withdrawn from the study if they are not acting according to the procedures 
described or are not respecting the conditions.  
We will start recruiting patients when approval of EC has been obtained.  
 
6. INFORMED CONSENT 
 
The participant must personally sign and date the latest approved version of the informed consent form 
before any study specific procedures are performed. Written and verbal versions of the Participant 
Information Sheet and Informed Consent will be presented to the participants detailing no less than: the 
exact nature of the study; the implications and constraints of the protocol; the known side effects and any 
risks involved in taking part. It will be clearly stated that the participant is free to withdraw from the study 
at any time for any reason without prejudice to future care, and with no obligation to give the reason for 
withdrawal. 

 
 
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7. COSTS AND COMPENSATION FOR PARTICIPATING  
 
Participation in this trial will not result in any additional cost to the patients. Patients do not receive 
compensations but transport will be reimbursed for visits that are not part of routine clinical practice.  
 
8. CONFIDENTIALITY 
In accordance with the Belgian law concerning the private life protection (08 Dec 1992) and the patient’s 
rights (22 Aug 2002) the information collected from participation in this study is protected. The participants 
have the right to request information of the existence of personal data held by the study coordinator and 
will have the right to rectify erroneous or inaccurate data. Representatives of the study coordinators, the 
Independent Ethical Committee and/or Regulatory Authorities will be granted direct access to the original 
medical records for verification of the clinical trial procedures and/or data, without violating the 
confidentiality according to the laws and regulations applicable in Belgium. By signing this informed 
consent form, participants are authorizing such access. 
From patients agreeing to participate in this study, personal data and clinical information will be collected 
and coded. No reports containing the personal data will be publicly available. 
9. ICH/GCP GUIDELINES 
 
This trial will be conducted in accordance with the protocol, current ICH-GCP guidelines and applicable 
law(s). Good Clinical Practice (GCP) is an international ethical and scientific quality standard for 
designing, conducting, recording and reporting trials that involve the participation of human subjects. 
Compliance with this standard provides public assurance that the rights, safety and well-being of trial 
subjects are protected, consistent with the principles that have their origin in the Declaration of Helsinki, 
and that the clinical trial data are credible. 
10. INSURANCE  
 
The coordinators of this study are liable, even without fault, for damage that the participants or legal 
successor has sustained and that has direct or indirect link with the trial. To that end the study has 
provided insurance coverage. The end of the study is defined as the sampling at the third time point.  
 
11. DISSEMINATION 
 
The study outcome and data will be published in peer-reviewed journals, aiming the highest impact factor 
in the field.  
 
12. CONTACT PERSON 
 
• Prof. Dr. VANDEKERCKHOVE LINOS  
Telephone :: 09/3323398 
Email : linos.vandekerckhove@uzgent.be 
• Dr. VAN DER MOEREN NATHALIE   

 
 
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Telephone : 0470888849 
Email : nathalie.vandermoeren@ugent.be 
 
 
 
 
 
Signature Page  
 
Investigator:  
 
Name: Prof. Dr. Linos Vandekerckhove  
 
Signature:  
 
Date: 29-06-2017