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Epidemiology of HIV infection

Since the last decade of last century, HIV/AIDS epidemic has become the greatest challenge in global health. Overall the number of HIV infected individuals has regularly increased. In 2012, it is estimated that 35.3 (range 32.2-38.8) million persons are living with HIV worldwide. It is estimated that 2.3 (range 1.9-2.7) million have became newly infected with HIV and 1.6 (range 1.4-1.9) million died in the year 2012 (Unaids, 2013) compared to 5.6 million new infections and 2.6 million deaths in the year 1999 (Cock KM et al, 2000). Nowadays, the global prevalence of HIV infection has decreased and stabilized at 0.8 % (range 0.7% – 0.9%) (Dorrucci M, 2010).
The global statistics on HIV infection mask some important local and regional epidemiologic differences. The sub-Saharan Africa remains the most heavily affected region, with two-thirds of the global burden. In addition, regional differences in the trends and mode of transmission exist: epidemics of HIV in men who have sex with men (MSM) continue to expand in most countries notably in the developed countries while heterosexual transmission remains the main mode of transmission in sub-Saharan Africa (Beyrer C et al, 2012). Worldwide HIV/AIDS prevalence is shown in figure 1.
In France, according to the French National Institute for Public Health Surveillance, it is estimated that 6400 individuals were newly diagnosed in the year 2012, a stable number since 2007. The number of newly diagnosed cases of HIV infection was stable in all groups except among MSM where the number increased and attributed to 42% of new diagnosed cases in 2012. The increasing number of newly diagnosed cases seems to be the result of a greater use of screening in this population including the use of rapid diagnostic tests (http://www.invs.sante.fr). The incidence of HIV infection was estimated at about 17 per 100 000 person-years. Even the incidence of HIV infection has decreased between 2003 and 2008, it remained high and stable in MSM with an incidence of 1006/100 000 person-years in MSM compared to 86/100 000 person-years in intravenous drug users and 9/100 000 person-years among heterosexuals (Le Vu S et al, 2010). In 2010, it was estimated that 149900 (95% CI; 134700-164900) HIV-infected persons were living in France. Of those, 81% were diagnosed while the remaining 19% ignored their seropositivity. While 74% of HIV-infected patients were receiving care, only 56% of them achieved controlled viral load. In addition, the proportions of diagnosed patients, those under care and those with a perfect response to antiretroviral therapy defined as achieving control of viral replication (controlled viral load) varied according the transmission mode. While the highest proportions were found among drug abusers, the lowest proportions were among non-French heterosexuals (Supervie V et al, CROI 2013, Abs. 1030).

Immune response against HIV infection

The first response against the HIV infection takes place at the site of infection in order to prevent viral entry. Mucosal epithelium mediates innate defenses through signaling system with Toll-like receptors and provides an array of inhibitory molecules such as SDF-1, MIP-1 α/β and RANTES (SDF-1 blocks CXCR4 while MIP-1 α/β and RANTES block CCR5). The vaginal inoculation of virus leads to the expression of chemokines (MIP-3α) that recruit interferon (IFN)-α/β producing plasmacytoid dendritic cells (pDCs) and to the production of pro-inflammatory cytokines (GM-CSF, IL-1, IL-6 and IL-8) that recruit neutrophils, macrophages and lymphocytes to the endocervix (Haase AT et al, 2010). The response of pDCs results in the induction of inflammatory cytokines, which are involved in directly setting up an antiviral state, and indirectly activating other antiviral cells of the innate immune system (Carrington M et al, 2012). Natural killer cells mediate antiviral control, through the recognition of virally infected cells through a network of receptors called the killer immunoglobulin-like receptors (Alter G et al, 2011).

The asymptomatic phase of HIV infection

Is a dynamic process of virus production and clearance by the immune responses which maintain HIV-RNA stabilized around a set point (Pantaleo G et al, 1995). As the immune response is not sufficient to control the virus, the replication continues in the presence of the activated immune system (clinical latency) and leads to slow and gradual depletion of CD4+ T lymphocytes count and this decline varies among individuals. Depending on a rate of CD4 decline between 50-100 cells/mm3 per year, the asymptomatic phase may last 10 years in some individuals. Without any symptoms, HIV-infected individual are however a source of contamination for their sexual partners.

The symptomatic phase:

Prior to the development of AIDS, the homeostasis between the viral replication and the immune responses breaks and leads to rapid depletion of the total T cells and eventually in immune collapse. The reason behind this break may be due to the exhaustion of the proliferative capacity of lymphocytes and progressive deterioration of lymphoid organs as well as the HIV-induced immune activation. It is in this phase where AIDS defining diseases such pneumocystis jirovecii pneumonia, Kaposi’s sarcoma and tuberculosis appear mainly when CD4 counts drop below 200 cells/mm3. Figure 7 illustrates the natural course of HIV infection.

Predictive biomarkers in the natural course of HIV infection

From the beginning of the epidemics, before being able to directly quantify virus production in blood, different biomarkers have been investigated as surrogate markers to predict HIV disease progression namely occurrence of AIDS, or death in the different attempts to identify drug targets for clinical interventions. These biomarkers could reflect the intensity of viral replication, the degree of immune system activation and the degree of immune deficiency. Beside the predictive value of CD4+ cell count and percentage, neopterin, B2-microglobulin (immune activation markers) and p24 antigen were identified as predictive biomarkers of HIV disease progression and all-cause mortality before the availability of viral load measurement. Later in 1995, the HIV-1 RNA revealed as strong predictor of HIV progression to AIDS and death independently of CD4+ lymphocyte count (Mellors JW et al, 1995; Mellors JW et al, 1997). Since then, CD4+ cell count and HIV-1 RNA are the most accurate predictive biomarkers in HIV infection and the standard investigation in HIV infected patients. In addition to markers of immune activation, different markers of inflammation (sICAM-1, E-selectin and IL-6) were predictive of all-cause mortality. In a cohort of 606 ART-naïve HIV-infected women, CRP was predictive of maternal progression to AIDS, maternal mortality and child mortality. Table 1 summarizes studies that investigated predictive biomarkers in the natural course of HIV infection in untreated HIV-infected patients.

Highly active antiretroviral therapy: the revolution

Since HIV was isolated in 1983, there has been intensive research to identify drugs that could inhibit viral production. Zidovudine, a nucleoside analogue reverse transcriptase inhibitor (NRTI) has been the first antiretroviral drug to demonstrate a benefit in clinical course of HIV disease (Fischl MA et al, 1987). However, the benefit was short term mainly due to the insufficient antiviral potency of this drug used as a monotherapy for a sustained clinical benefit. With the continuing development of drugs in the same class, the next step has been the evaluation of dual NRTI combination. Combination therapy with zidovudine and didanosine produced better outcomes in terms of virological control and CD4+ cell counts increases than zidovudine therapy alone (Collier AC et al, 1993). Similar results were obtained when combining zidovudine and lamivudine (Eron JJ et al, 1995). In 1996, for the first time, the combination of three dugs with the combination of 2 NRTIs and a protease inhibitor (Murphy RL et al, 2001) followed soon by the non-nucleoside analogue reverse transcriptase inhibitor (NNRTI) class as third agent, led to a durable clinical benefit and durable control of viral replication (Rey D et al, 2001) with a massive decrease in AIDS incidence and mortality. With the concomitant development of virological assays allowing direct quantification of viral replication and therefore the measurement of viral control, antiretroviral strategy has entered a new era. The concept of highly active antiretroviral therapy (HAART) or combined antiretroviral therapy (cART) was born and remains the gold standard. By controlling viral replication, cART allows immune restoration, prevent occurrence of viral resistance and reduces viral transmission (Palella FJ Jr et al, 2006; Grinsztejn B et al, 2014).

Recommendations for first-line cART initiation

The question of “when to start” antiretroviral therapy has been debated for many years and still differs in the different guidelines even across countries and particularly since the advent of combined ART. The dramatic effects of combination antiretroviral therapy which was introduced in 1996 on mortality and morbidity, coupled with emerging insights regarding viral dynamics and HIV evolution, supported the interest of early initiation of therapy. The “hit HIV, early and hard” paradigm was adopted in the US Department of Health and Human Services (DHHS) guidelines between 1998 and 2000, which recommended that most patients be offered therapy, including those with asymptomatic disease and a CD4+ cell count above 500 cells/mm3 (US DHHS guidelines, 2000). However, after the early enthusiasm of late nineties, the recognition of metabolic toxicity, renal disorders, the fear about the development of resistance, the potential difficulties of implementing ART in all patients from all countries who need it, a switch happened and guidelines went back in their recommendation questioning whether potential benefits of therapy outweighed the potential risks at higher CD4+ cell counts. This led to the sense that medications should be delayed. Several cohort studies during this era indicated that a higher pre-treatment CD4+ cell count was a strong predictor of good outcomes during therapy, with consistent and clear benefits occurring if therapy was initiated before the CD4 declined to below 200 cells/ mm3, but additional benefit was also apparent when therapy was initiated at a CD4 of 200 to 350 cells/ mm3 (Hogg RS et al, 2001; Egger M et al, 2002; Palella FJ et al, 2003). The 2001 version of the DHHS guidelines was modified accordingly such that therapy was strongly recommended for those with a CD4 <200 cells/ mm3, generally recommended for those with a CD4 count of 200 to 350 cells/ mm3 and not recommended in patients with higher CD4 cell counts (US DHHS guidelines, 2001).
In the recent years, the availability of well tolerated, less toxic and co-formulated antiretroviral drugs made the rationale for delaying antiretroviral therapy less evident. The SMART study (El-Sadr WM et al, 2006) has been a key study that has deeply modified the concepts about HIV clinical pathogenesis. This study randomized HIV-infected patients who had a CD4+ cell count of more than 350/mm3 to the continuous use or episodic use of antiretroviral therapy. Episodic use involved the deferral of therapy until the CD4+ count decreased to less than 250/mm3 and then the use of therapy until the CD4+ count increase to more than 350/mm3. Opportunistic diseases or death from any cause occurred more in the interruption use group compared to the continuous use group. The risk of all-cause mortality was associated with high levels of inflammation and coagulation biomarkers suggesting that interrupting therapy may increase the risk of death (Kuller LH et al, 2008). Recent recommendations delivered in 2012 recommend treatment for all HIV-infected individuals with different strength of recommendations (US DHHS guidelines, 2012) and the concept “Treatment as prevention’ was adopted in the last guidelines delivered in 2013 which recommend that antiretroviral therapy should be started if a patient is requesting treatment and ready to start, and in sero-different partners to decrease HIV transmission. Table 3 shows different recommendations on when to start antiretroviral therapy according to different guidelines.

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HIV replication control and immune system restoration

Nowadays, we are in the era where most of HIV-infected patients who have access to ART have achieved controlled plasmatic viral loads. Data from the FHDH shows that 89% of patients under cART in the year 2012 achieved controlled viremia (<50 copies/mL) compared to 79% in the year 2007. The control of HIV viremia has a substantial role in the management of HIV infection and its consequences.
The control of viremia has been translated in a series of immunological and clinical benefits. The restoration of CD4+ cell count occurs following the initiation of cART and a rise of 50 to 100 cells/mm3 is usually observed in the first year of therapy. In a long term observational study that prospectively followed patients initiating cART, the majority of increase in CD4 cell counts was in the first two years with little increase afterwards (Lok JJ et al, 2010). In some patients, the viral suppression under ART is not associated with CD4 count restoration, a phenomenon that is predictive of worse outcomes. Controlled viral load and restored immunity on combination antiretroviral therapy (cART) resulted in significant differences in the incidence of AIDS-defining illnesses (esophageal candidiasis, Kaposi’s sarcoma, pulmonary and extrapulmonary tuberculosis, non-Hodgkins lymphoma, bacterial pneumonia, Pneumocystis jirovecii pneumonia and recurrent herpes simplex) before and after cART as well as over the different periods of cART (Mocroft A et al, 2013; Hleyhel M et al, 2013).
In addition to the immunological and clinical benefits, the control of viremia (<50copies/mL) has been shown to prevent the selection of resistance mutations by the HIV. In patients with persistent low-level viremia under cART, new resistance mutations were detected and the magnitude of low-level viremia was the primary driver of evolution rate at emergent drug resistance mutation (Taiwo B et al, 2011; Vardhanabhuti S et al, 2014).

Decreased mortality and morbidity with increased survival probabilities

Since the introduction of cART, dramatic decrease in the overall mortality has been observed (Mocroft A et al, 2003; Palella FJ Jr, 2003). A recent study compared mortality rates in the SMART and ESPRIT trials with the mortality rates in the general population. Patients who were not users of injection drugs, aged 20-70 years, from the continuous ART control arms of ESPRIT and SMART, were included if the HIV plasma viral load was ≤400 copies/ml in the SMART study and ≤500 copies/ml in the ESPRIT study. Mortality rate was increased compared with the general population with a CD4+ cell count between 350 and 499 cells/mm3 [SMR 1.77, 95% CI 1.17-2.55] while no evidence for increased mortality was seen with CD4+ cell counts greater than 500 cells/mm3 (SMR 1.00, 95% CI 0.69-1.40) (Rodger AJ et al, 2013).
Along with the decrease in mortality, survival probabilities among HIV-infected patients initiating effective cART increased. In the UK Collaborative HIV Cohort Study where patients aged more than 20 years who started ART during 2000-2010 (excluding injection drugs users), were followed for mortality until 2012, the expected age at death of 35-year-old men with CD4 cell count of at least 350 cells/mm3 was 77 (72-81) years, compared with 78 years for men in the general UK population (May MT et al, 2014). These results suggest that newly diagnosed, successfully treated individuals can have a normal life expectancy.

Table of contents :

I. RESUME DES TRAVAUX DE THESE
II. SCIENTIFIC PRODUCTION
III. ABBREVIATIONS LIST
IV. INTRODUCTION
V. STATE OF THE ART
A. Human immunodeficiency virus (HIV)
1. Epidemiology of HIV infection
2. HIV replication cycle
3. Immune response against HIV infection
4. The natural course of HIV-1 infection
5. Predictive biomarkers in the natural course of HIV infection
B. Highly active antiretroviral therapy: the revolution
1. Classes of antiretroviral therapy
2. Recommendations for first-line cART initiation
3. Benefits of antiretroviral therapy (ART)
4. Complications of cART
C. Beyond cART: failure of eradication, residual viremia and persistent immune activation and inflammation
1. HIV reservoirs and failure of eradication
2. Residual viremia
3. Persistent immune activation and inflammation among HIV-infected patients
VI. MATERIALS AND METHODS
A. Hypothesis and objectives of the study
1. Hypothesis
2. Objectives
B. Study design
1. Inclusion criteria of patients
2. Non-inclusion criteria
3. Controls
4. Ethical aspects
C. Database resources
1. Department of infectious diseases/ Pitié-Salpétrière hospital
2. NADIS®
D. Patients selection, clinical data collection and exportation
E. Plasma collection and preparation
F. Biomarkers selection and measurement
1. Enzyme-Linked ImmunoSorbent Assay (ELISA)
2. Cytometric Bead Array (CBA)
G. Statistical analyses
1. Relationships between biomarker levels and patients characteristics at cART initiation
2. Changes in biomarker levels after two years of effective cART
3. Factors associated with persistent elevated marker levels after 2 years of cART
4. Comparative impact of different ART components on the evolution of biomarkers
5. Sensitivity analyses
VII. RESULTS
A. Impact of two years of effective first-line cART on soluble biomarkers of immune activation and inflammation
1. Summary of the study
2. Submitted article 1
3. Supplementary data
B. Comparative impact of different ART components on the evolution of immune activation and inflammation markers
1. Summary of the study
2. Published article 2
3. Supplementary data
VIII. DISCUSSION
IX. CONCLUSIONS AND PERSPECTIVES
X. BIBLIOGRAPHY

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