M. J. Ploquin, G. Silvestri, and M. Muller-trutwin, Immune activation in HIV infection, Current Opinion in HIV and AIDS, vol.11, issue.2, pp.201-209, 2016.
DOI : 10.1097/COH.0000000000000238
URL : https://hal.archives-ouvertes.fr/pasteur-01289403

L. H. Kuller, R. Tracy, W. Belloso, D. Wit, S. Drummond et al., Inflammatory and Coagulation Biomarkers and Mortality in Patients with HIV Infection, PLoS Medicine, vol.180, issue.10, p.18942885, 2008.
DOI : 10.1371/journal.pmed.0050203.sd002

R. Rajasuriar, E. Wright, and L. S. , Impact of antiretroviral therapy (ART) timing on chronic immune activation/inflammation and end-organ damage, Current Opinion in HIV and AIDS, vol.10, issue.1, pp.35-42, 2015.
DOI : 10.1097/COH.0000000000000118

N. G. Sandler and D. C. Douek, Microbial translocation in HIV infection: causes, consequences and treatment opportunities, Nature Reviews Microbiology, vol.10, issue.9, pp.655-66, 2012.
DOI : 10.1038/nrmicro2848

J. M. Brenchley, M. Paiardini, K. S. Knox, A. I. Asher, B. Cervasi et al., Differential Th17 CD4 T-cell depletion in pathogenic and nonpathogenic lentiviral infections, Blood, vol.112, issue.7, pp.2826-2861, 2008.
DOI : 10.1182/blood-2008-05-159301

J. D. Estes, L. D. Harris, N. R. Klatt, B. Tabb, S. Pittaluga et al., Damaged Intestinal Epithelial Integrity Linked to Microbial Translocation in Pathogenic Simian Immunodeficiency Virus Infections, PLoS Pathogens, vol.434, issue.8, p.20808901, 2010.
DOI : 10.1371/journal.ppat.1001052.s011

I. V. Pandrea, R. Gautam, R. M. Ribeiro, J. M. Brenchley, I. F. Butler et al., Acute Loss of Intestinal CD4+ T Cells Is Not Predictive of Simian Immunodeficiency Virus Virulence, The Journal of Immunology, vol.179, issue.5, pp.179-3035, 2007.
DOI : 10.4049/jimmunol.179.5.3035

M. Paiardini, I. Frank, I. Pandrea, C. Apetrei, and G. Silvestri, Mucosal immune dysfunction in AIDS pathogenesis, AIDS Rev, vol.10, issue.1, pp.36-46, 2008.

S. E. Bosinger, Q. Li, S. N. Gordon, N. R. Klatt, L. Duan et al., Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys. The Journal of clinical investigation, pp.119-3556, 2009.

L. Campillo-gimenez, M. Laforge, M. Fay, A. Brussel, M. C. Cumont et al., Nonpathogenesis of Simian Immunodeficiency Virus Infection Is Associated with Reduced Inflammation and Recruitment of Plasmacytoid Dendritic Cells to Lymph Nodes, Not to Lack of an Interferon Type I Response, during the Acute Phase, Journal of Virology, vol.84, issue.4, pp.1838-1884, 2010.
DOI : 10.1128/JVI.01496-09

O. M. Diop, M. J. Ploquin, L. Mortara, A. Faye, B. Jacquelin et al., Plasmacytoid Dendritic Cell Dynamics and Alpha Interferon Production during Simian Immunodeficiency Virus Infection with a Nonpathogenic Outcome, Journal of Virology, vol.82, issue.11, pp.82-5145, 2008.
DOI : 10.1128/JVI.02433-07
URL : https://hal.archives-ouvertes.fr/hal-00345347

L. D. Harris, B. Tabb, D. L. Sodora, M. Paiardini, N. R. Klatt et al., Downregulation of Robust Acute Type I Interferon Responses Distinguishes Nonpathogenic Simian Immunodeficiency Virus (SIV) Infection of Natural Hosts from Pathogenic SIV Infection of Rhesus Macaques, Journal of Virology, vol.84, issue.15, pp.84-7886, 2010.
DOI : 10.1128/JVI.02612-09

J. B. Mayau, V. Targat, B. Liovat, A. S. Kunkel, D. Petitjean et al., Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response, The Journal of clinical investigation, issue.12, pp.119-3544, 2009.

J. B. Petitjean, G. Kunkel, D. Liovat, A. S. Jochems, S. P. Rogers et al., Innate immune responses and rapid control of inflammation in African green monkeys treated or not with interferon-alpha during primary SIVagm infection, PLoS Pathog, vol.10, issue.7, p.24991927, 2014.

C. Kornfeld, M. J. Ploquin, I. Pandrea, A. Faye, R. Onanga et al., Antiinflammatory profiles during primary SIV infection in African green monkeys are associated with protection against AIDS, Journal of Clinical Investigation, vol.115, issue.4, pp.1082-91, 2005.
DOI : 10.1172/JCI23006

O. M. Diop, A. Gueye, M. Dias-tavares, C. Kornfeld, A. Faye et al., High Levels of Viral Replication during Primary Simian Immunodeficiency Virus SIVagm Infection Are Rapidly and Strongly Controlled in African Green Monkeys, Journal of Virology, vol.74, issue.16, pp.74-7538, 2000.
DOI : 10.1128/JVI.74.16.7538-7547.2000

A. S. Liovat, M. A. Rey-cuille, C. Lecuroux, B. Jacquelin, I. Girault et al., Acute Plasma Biomarkers of T Cell Activation Set-Point Levels and of Disease Progression in HIV-1 Infection, PLoS ONE, vol.7, issue.10, p.23056251, 2012.
DOI : 10.1371/journal.pone.0046143.s007

A. Durudas, H. L. Chen, M. A. Gasper, V. Sundaravaradan, J. M. Milush et al., Differential Innate Immune Responses to Low or High Dose Oral SIV Challenge in Rhesus Macaques, Current HIV Research, vol.9, issue.5, pp.276-88, 2011.
DOI : 10.2174/157016211797635928

R. P. Simmons, E. P. Scully, E. E. Groden, K. B. Arnold, J. J. Chang et al., HIV-1 infection induces strong production of IP-10 through TLR7/9-dependent pathways, AIDS, vol.27, issue.16, pp.2505-2522, 2013.
DOI : 10.1097/01.aids.0000432455.06476.bc

K. Allers, M. Fehr, K. Conrad, H. J. Epple, D. Schurmann et al., Macrophages Accumulate in the Gut Mucosa of Untreated HIV-infected Patients, Journal of Infectious Diseases, vol.209, issue.5, pp.739-787, 2014.
DOI : 10.1093/infdis/jit547

A. Zalar, M. I. Figueroa, B. Ruibal-ares, P. Bare, P. Cahn et al., Macrophage HIV-1 infection in duodenal tissue of patients on long term HAART, Antiviral Research, vol.87, issue.2, pp.269-71, 2010.
DOI : 10.1016/j.antiviral.2010.05.005

A. Gosselin, P. Monteiro, N. Chomont, F. Diaz-griffero, E. A. Said et al., Peripheral Blood CCR4+CCR6+ and CXCR3+CCR6+ CD4+ T Cells Are Highly Permissive to HIV-1 Infection, The Journal of Immunology, vol.184, issue.3, pp.184-1604, 2010.
DOI : 10.4049/jimmunol.0903058

J. F. Foley, C. Yu, R. Solow, M. Yacobucci, K. W. Peden et al., Roles for CXC Chemokine Ligands 10 and 11 in Recruiting CD4+ T Cells to HIV-1-Infected Monocyte-Derived Macrophages, Dendritic Cells, and Lymph Nodes, The Journal of Immunology, vol.174, issue.8, pp.174-4892, 2005.
DOI : 10.4049/jimmunol.174.8.4892

T. H. Burdo, M. R. Lentz, P. Autissier, A. Krishnan, E. Halpern et al., Soluble CD163 Made by Monocyte/Macrophages Is a Novel Marker of HIV Activity in Early and Chronic Infection Prior to and After Anti-retroviral Therapy, Journal of Infectious Diseases, vol.204, issue.1, pp.154-63, 2011.
DOI : 10.1093/infdis/jir214

N. G. Sandler and I. Sereti, Can early therapy reduce inflammation?, Current Opinion in HIV and AIDS, vol.9, issue.1, p.24247669
DOI : 10.1097/COH.0000000000000020

J. D. Lundgren, A. G. Babiker, F. Gordin, S. Emery, B. Grund et al., Initiation of Antiretroviral Therapy in Early Asymptomatic HIV Infection, N Engl J Med, issue.9, pp.373-795, 1056.

T. Bruel, C. Hamimi, N. Dereuddre-bosquet, A. Cosma, S. Y. Shin et al., ABSTRACT, Journal of Virology, vol.89, issue.7, pp.89-3542, 2015.
DOI : 10.1128/JVI.03723-14

O. Bourry, A. Mannioui, P. Sellier, C. Roucairol, L. Durand-gasselin et al., Effect of a short-term HAART on SIV load in macaque tissues is dependent on time of initiation and antiviral diffusion, Retrovirology, vol.7, issue.1, p.20868521
DOI : 10.1186/1742-4690-7-78
URL : https://hal.archives-ouvertes.fr/inserm-00668445

S. Beq, M. T. Nugeyre, R. Ho-tsong-fang, D. Gautier, R. Legrand et al., IL-7 induces immunological improvement in SIVinfected rhesus macaques under antiviral therapy, Journal of immunology, issue.2, pp.176-914, 2006.
URL : https://hal.archives-ouvertes.fr/pasteur-00023330

A. Gueye, O. M. Diop, M. J. Ploquin, C. Kornfeld, A. Faye et al., Viral load in tissues during the early and chronic phase of non-pathogenic SIVagm infection, Journal of Medical Primatology, vol.10, issue.2, pp.33-83, 2004.
DOI : 10.1128/JVI.76.10.5271-5273.2002

A. M. Mowat and A. W. , Regional specialization within the intestinal immune system, Nature Reviews Immunology, vol.12, issue.10, pp.14-667, 2014.
DOI : 10.1111/j.1749-6632.2010.05708.x

A. Antonelli, S. M. Ferrari, D. Giuggioli, E. Ferrannini, C. Ferri et al., Chemokine (C???X???C motif) ligand (CXCL)10 in autoimmune diseases, Autoimmunity Reviews, vol.13, issue.3, p.24189283, 2014.
DOI : 10.1016/j.autrev.2013.10.010

C. M. Hilkens, J. F. Schlaak, and I. M. Kerr, Differential responses to IFN-alpha subtypes in human T cells and dendritic cells, J Immunol, issue.10, pp.171-5255, 2003.

J. Wenzel, E. Worenkamper, S. Freutel, S. Henze, O. Haller et al., Enhanced type I interferon signalling promotes Th1-biased inflammation in cutaneous lupus erythematosus, The Journal of Pathology, vol.71, issue.4, pp.435-477, 2005.
DOI : 10.1002/path.1721

M. Mavigner, M. Cazabat, M. Dubois, F. E. L-'faqihi, M. Requena et al., Altered CD4+ T cell homing to the gut impairs mucosal immune reconstitution in treated HIV-infected individuals, Journal of Clinical Investigation, vol.122, issue.1, pp.62-71, 2012.
DOI : 10.1172/JCI59011DS1

D. J. Hartigan-o-'connor, L. A. Hirao, J. M. Mccune, and S. Dandekar, Th17 cells and regulatory T cells in elite control over HIV and SIV, Current Opinion in HIV and AIDS, vol.6, issue.3, pp.221-228, 2011.
DOI : 10.1097/COH.0b013e32834577b3

M. J. Ploquin, J. F. Desoutter, P. R. Santos, I. Pandrea, O. M. Diop et al., Distinct expression profiles of TGF-beta1 signaling mediators in pathogenic SIVmac and non-pathogenic SIVagm infections, Retrovirology, issue.3, pp.37-16800882, 2006.
URL : https://hal.archives-ouvertes.fr/inserm-00089761

V. Cecchinato, C. J. Trindade, A. Laurence, J. M. Heraud, J. M. Brenchley et al., Altered balance between Th17 and Th1 cells at mucosal sites predicts AIDS progression in simian immunodeficiency virus-infected macaques, Mucosal Immunology, vol.417, issue.4, pp.279-88, 2008.
DOI : 10.1038/mi.2008.14

D. Favre, S. Lederer, B. Kanwar, Z. M. Ma, S. Proll et al., Critical Loss of the Balance between Th17 and T Regulatory Cell Populations in Pathogenic SIV Infection, PLoS Pathogens, vol.14, issue.2, 2009.
DOI : 10.1371/journal.ppat.1000295.s010

M. P. Berry, C. M. Graham, F. W. Mcnab, Z. Xu, S. A. Bloch et al., An interferon-inducible neutrophildriven blood transcriptional signature in human tuberculosis, Nature, issue.7309, pp.466-973, 1038.

M. D. Hazenberg, S. A. Otto, B. H. Van-benthem, M. T. Roos, R. A. Coutinho et al., Persistent immune activation in HIV-1 infection is associated with progression to AIDS, AIDS, vol.17, issue.13, pp.17-1881, 2003.
DOI : 10.1097/00002030-200309050-00006

J. Lajoie, J. Juno, A. Burgener, S. Rahman, K. Mogk et al., A distinct cytokine and chemokine profile at the genital mucosa is associated with HIV-1 protection among HIV-exposed seronegative commercial sex workers, Mucosal Immunology, vol.171, issue.3, pp.277-87, 2012.
DOI : 10.1074/jbc.R100016200

J. Lajoie, M. Kimani, F. A. Plummer, F. Nyamiobo, R. Kaul et al., Association of Sex Work With Reduced Activation of the Mucosal Immune System, Journal of Infectious Diseases, vol.210, issue.2, pp.319-348, 2014.
DOI : 10.1093/infdis/jiu023

E. M. Kahle, M. Bolton, J. P. Hughes, D. Donnell, C. Celum et al., Plasma Cytokine Levels and Risk of HIV Type 1 (HIV-1) Transmission and Acquisition: A Nested Case-Control Study Among HIV-1-Serodiscordant Couples, Journal of Infectious Diseases, vol.211, issue.9, pp.211-1451, 2015.
DOI : 10.1093/infdis/jiu621

A. Cheret, G. Nembot, A. Melard, C. Lascoux, L. Slama et al., Intensive five-drug antiretroviral therapy regimen versus standard triple-drug therapy during primary HIV-1 infection (OPTIPRIM-ANRS 147): a randomised, open-label, phase 3 trial, The Lancet Infectious Diseases, vol.15, issue.4, pp.387-96, 2015.
DOI : 10.1016/S1473-3099(15)70021-6
URL : https://hal.archives-ouvertes.fr/pasteur-01420416

S. Qin, F. Junecko, B. A. Trichel, A. M. Tarwater, P. M. Murphey-corb et al., Simian Immunodeficiency Virus Infection Alters Chemokine Networks in Lung Tissues of Cynomolgus Macaques, The American Journal of Pathology, vol.177, issue.3, pp.1274-85, 2010.
DOI : 10.2353/ajpath.2010.091288

T. A. Reinhart, B. A. Fallert, M. E. Pfeifer, S. Sanghavi, S. Capuano et al., Increased expression of the inflammatory chemokine CXC chemokine ligand 9/monokine induced by interferon-gamma in lymphoid tissues of rhesus macaques during simian immunodeficiency virus infection and acquired immunodeficiency syndrome, Blood, vol.99, issue.9, pp.99-3119, 2002.
DOI : 10.1182/blood.V99.9.3119

M. P. Lemos, J. R. Lama, S. T. Karuna, Y. Fong, S. M. Montano et al., The Inner Foreskin of Healthy Males at Risk of HIV Infection Harbors Epithelial CD4+ CCR5+ Cells and Has Features of an Inflamed Epidermal Barrier, PLoS ONE, vol.19, issue.9, p.25268493, 2014.
DOI : 10.1371/journal.pone.0108954.s001

P. U. Cameron, S. Saleh, G. Sallmann, A. Solomon, F. Wightman et al., Establishment of HIV-1 latency in resting CD4+ T cells depends on chemokineinduced changes in the actin cytoskeleton, Proc Natl Acad Sci, issue.39, pp.107-16934, 2010.

C. Heise, P. Vogel, C. J. Miller, C. H. Halsted, and S. Dandekar, Simian immunodeficiency virus infection of the gastrointestinal tract of rhesus macaques. Functional, pathological, and morphological changes

R. S. Veazey, M. Demaria, L. V. Chalifoux, D. E. Shvetz, D. R. Pauley et al., Gastrointestinal Tract as a Major Site of CD4+ T Cell Depletion and Viral Replication in SIV Infection, Science, vol.280, issue.5362, pp.280-427, 1998.
DOI : 10.1126/science.280.5362.427

S. A. Yukl, S. Gianella, E. Sinclair, L. Epling, Q. Li et al., Differences in HIV burden and immune activation within the gut of HIVpositive patients receiving suppressive antiretroviral therapy, J Infect Dis, issue.10, pp.202-1553, 2010.

S. A. Yukl, A. K. Shergill, T. Ho, M. Killian, V. Girling et al., The Distribution of HIV DNA and RNA in Cell Subsets Differs in Gut and Blood of HIV-Positive Patients on ART: Implications for Viral Persistence, Journal of Infectious Diseases, vol.208, issue.8, pp.208-1212, 2013.
DOI : 10.1093/infdis/jit308

T. A. Angelovich, A. C. Hearps, A. Maisa, G. E. Martin, G. F. Lichtfuss et al., Viremic and Virologically Suppressed HIV Infection Increases Age-Related Changes to Monocyte Activation Equivalent to 12 and 4 Years of Aging, Respectively, JAIDS Journal of Acquired Immune Deficiency Syndromes, vol.69, issue.1, pp.11-18, 2015.
DOI : 10.1097/QAI.0000000000000559

P. Nigam, S. Kwa, V. Velu, and A. R. , Loss of IL-17-Producing CD8 T Cells during Late Chronic Stage of Pathogenic Simian Immunodeficiency Virus Infection, The Journal of Immunology, vol.186, issue.2, pp.745-53, 2011.
DOI : 10.4049/jimmunol.1002807

N. Noel, F. Boufassa, C. Lecuroux, A. Saez-cirion, C. Bourgeois et al., Elevated IP10 levels are associated with immune activation and low CD4+ T-cell counts in HIV controller patients, AIDS, vol.28, issue.4, pp.467-76, 2014.
DOI : 10.1097/QAD.0000000000000174
URL : https://hal.archives-ouvertes.fr/pasteur-01420524

N. Noel, N. Lerolle, C. Lecuroux, C. Goujard, A. Venet et al., Immunologic and Virologic Progression in HIV Controllers: The Role of Viral ???Blips??? and Immune Activation in the ANRS CO21 CODEX Study, PLOS ONE, vol.9, issue.7, p.26146823, 2015.
DOI : 10.1371/journal.pone.0131922.s001
URL : https://hal.archives-ouvertes.fr/pasteur-01415218

Z. Euler, M. J. Van-gils, B. D. Boeser-nunnink, H. Schuitemaker, and D. Van-manen, Genome-Wide Association Study on the Development of Cross-Reactive Neutralizing Antibodies in HIV-1 Infected Individuals, PLoS ONE, vol.9, issue.1, p.23372753, 2013.
DOI : 10.1371/journal.pone.0054684.t002

C. Legeai, C. Vigouroux, J. C. Souberbielle, O. Bouchaud, F. Boufassa et al., Associations between 25-Hydroxyvitamin D and Immunologic, Metabolic, Inflammatory Markers in Treatment-Naive HIV-Infected Persons: The ANRS CO9 ??COPANA?? Cohort Study, PLoS ONE, vol.23, issue.12, p.24058636, 2013.
DOI : 10.1371/journal.pone.0074868.s001

J. Ghosn, I. Pellegrin, C. Goujard, C. Deveau, J. P. Viard et al., HIV-1 resistant strains acquired at the time of primary infection massively fuel the cellular reservoir and persist for lengthy periods of time, AIDS, vol.20, issue.2, pp.159-70, 2006.
DOI : 10.1097/01.aids.0000199820.47703.a0

C. Goujard, M. Bonarek, L. Meyer, F. Bonnet, M. L. Chaix et al., CD4 Cell Count and HIV DNA Level Are Independent Predictors of Disease Progression after Primary HIV Type 1 Infection in Untreated Patients, Clinical Infectious Diseases, vol.42, issue.5, pp.42-709, 2006.
DOI : 10.1086/500213

M. Laanani, J. Ghosn, A. Essat, A. Melard, R. Seng et al., Impact of the Timing of Initiation of Antiretroviral Therapy During Primary HIV-1 Infection on the Decay of Cell-Associated HIV-DNA, Clinical Infectious Diseases, vol.60, issue.11, pp.60-1715, 2015.
DOI : 10.1093/cid/civ171

N. Ngo-giang-huong, C. Deveau, D. Silva, I. Pellegrin, I. Venet et al., Proviral HIV-1 DNA in subjects followed since primary HIV-1 infection who suppress plasma viral load after one year of highly active antiretroviral therapy, AIDS, vol.15, issue.6, pp.15-665, 2001.
DOI : 10.1097/00002030-200104130-00001

C. J. Cohen, S. Q. Crome, K. G. Macdonald, E. L. Dai, D. L. Mager et al., Human Th1 and Th17 Cells Exhibit Epigenetic Stability at Signature Cytokine and Transcription Factor Loci, The Journal of Immunology, vol.187, issue.11, pp.5615-5641, 2011.
DOI : 10.4049/jimmunol.1101058

S. Q. Crome, B. Clive, A. Y. Wang, C. Y. Kang, V. Chow et al., Inflammatory Effects of Ex Vivo Human Th17 Cells Are Suppressed by Regulatory T Cells, The Journal of Immunology, vol.185, issue.6, pp.185-3199, 2010.
DOI : 10.4049/jimmunol.1000557

C. Rouzioux, A. Melard, A. , and V. , Quantification of Total HIV1-DNA in Peripheral Blood Mononuclear Cells, Methods Mol Biol, p.24158829
DOI : 10.1007/978-1-62703-670-2_21