L. Micci, Interleukin-21 combined with ART reduces inflammation and viral reservoir in SIV-infected macaques, Journal of Clinical Investigation, vol.125, issue.12, pp.4497-4513, 2015.
DOI : 10.1172/JCI81400DS1

J. B. Whitney, Rapid seeding of the viral reservoir prior to SIV viraemia in rhesus monkeys, Nature, vol.72, pp.74-77, 2014.
DOI : 10.1128/JVI.00512-12

H. Li, Hypercytotoxicity and Rapid Loss of NKp44+ Innate Lymphoid Cells during Acute SIV Infection, PLoS Pathogens, vol.85, issue.451, p.1004551, 2014.
DOI : 10.1371/journal.ppat.1004551.s006

H. Xu, X. Wang, A. A. Lackner, and R. S. Veazey, Type 3 innate lymphoid cell depletion is mediated by TLRs in lymphoid tissues of simian immunodeficiency virus-infected macaques. The FASEB Journal29, pp.5072-5080, 2015.

M. J. Ploquin, G. Silvestri, and M. Müller-trutwin, Immune activation in HIV infection, Current Opinion in HIV and AIDS, vol.11, issue.2, pp.201-208, 2016.
DOI : 10.1097/COH.0000000000000238

URL : https://hal.archives-ouvertes.fr/pasteur-01289403

S. N. Gordon, Severe Depletion of Mucosal CD4+ T Cells in AIDS-Free Simian Immunodeficiency Virus-Infected Sooty Mangabeys, The Journal of Immunology, vol.179, issue.5, pp.3026-3034, 2007.
DOI : 10.4049/jimmunol.179.5.3026

I. V. Pandrea, Acute Loss of Intestinal CD4+ T Cells Is Not Predictive of Simian Immunodeficiency Virus Virulence, The Journal of Immunology, vol.179, issue.5, pp.3035-3046, 2007.
DOI : 10.4049/jimmunol.179.5.3035

J. D. Estes, Damaged Intestinal Epithelial Integrity Linked to Microbial Translocation in Pathogenic Simian Immunodeficiency Virus Infections, PLoS Pathogens, vol.434, issue.8, p.1001052, 2010.
DOI : 10.1371/journal.ppat.1001052.s011

URL : http://doi.org/10.1371/journal.ppat.1001052

J. M. Brenchley, Differential Th17 CD4 T-cell depletion in pathogenic and nonpathogenic lentiviral infections, Blood, vol.112, issue.7, pp.2826-2835, 2008.
DOI : 10.1182/blood-2008-05-159301

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556618

O. M. Diop, 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.7538-7547, 2000.
DOI : 10.1128/JVI.74.16.7538-7547.2000

J. D. Estes, A. T. Haase, and T. W. Schacker, The role of collagen deposition in depleting CD4+ T cells and limiting reconstitution in HIV-1 and SIV infections through damage to the secondary lymphoid organ niche, Seminars in Immunology, vol.20, issue.3, pp.181-186, 2008.
DOI : 10.1016/j.smim.2008.04.002

E. Costa and H. , The local environment orchestrates mucosal decidual macrophage differentiation and substantially inhibits HIV-1 replication. Mucosal Immunol9, pp.634-646, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01453433

K. T. Arrildt, ABSTRACT, Journal of Virology, vol.89, issue.22, pp.11294-11311, 2015.
DOI : 10.1128/JVI.00946-15

S. Goldstein, Wide Range of Viral Load in Healthy African Green Monkeys Naturally Infected with Simian Immunodeficiency Virus, Journal of Virology, vol.74, issue.24, pp.11744-11753, 2000.
DOI : 10.1128/JVI.74.24.11744-11753.2000

J. M. Milush, Lack of clinical AIDS in SIV-infected sooty mangabeys with significant CD4+ T cell loss is associated with double-negative T cells, Journal of Clinical Investigation, vol.121, issue.3, pp.1102-1110, 2011.
DOI : 10.1172/JCI44876DS1

N. R. Klatt, Availability of activated CD4+ T cells dictates the level of viremia in naturally SIV-infected sooty mangabeys, Journal of Clinical Investigation, vol.118, pp.2039-2049, 2008.
DOI : 10.1172/JCI33814DS1

A. M. Ortiz, Depletion of CD4+ T cells abrogates post-peak decline of viremia in SIV-infected rhesus macaques, Journal of Clinical Investigation, vol.121, issue.11, pp.4433-4445, 2011.
DOI : 10.1172/JCI46023DS1

L. Micci, CD4 Depletion in SIV-Infected Macaques Results in Macrophage and Microglia Infection with Rapid Turnover of Infected Cells, PLoS Pathogens, vol.165, issue.10, p.1004467, 2014.
DOI : 10.1371/journal.ppat.1004467.s004

K. D. Mir, ABSTRACT, Journal of Virology, vol.89, issue.20, pp.10136-10144, 2015.
DOI : 10.1128/JVI.00710-15

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.655-666, 2012.
DOI : 10.1038/nrmicro2848

S. V. Westmoreland, SIV Vpx Is Essential for Macrophage Infection but Not for Development of AIDS, PLoS ONE, vol.5, issue.1, p.84463, 2014.
DOI : 10.1371/journal.pone.0084463.s001

L. H. Kuller, Inflammatory and Coagulation Biomarkers and Mortality in Patients with HIV Infection, PLoS Medicine, vol.180, issue.10, p.203, 2008.
DOI : 10.1371/journal.pmed.0050203.sd002

URL : http://doi.org/10.1371/journal.pmed.0050203

A. R. Tenorio, Soluble Markers of Inflammation and Coagulation but Not T-Cell Activation Predict Non-AIDS-Defining Morbid Events During Suppressive Antiretroviral Treatment, Journal of Infectious Diseases, vol.210, issue.8, pp.1248-1259, 2014.
DOI : 10.1093/infdis/jiu254

A. León, Association of microbial translocation biomarkers with clinical outcome in controllers HIV-infected patients, AIDS, vol.29, issue.6, pp.675-681, 2015.
DOI : 10.1097/QAD.0000000000000596

J. M. Brenchley, Mucosal immunity in human and simian immunodeficiency lentivirus infections. Mucosal Immunol6, pp.657-665, 2013.
DOI : 10.1038/mi.2013.15

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154146

J. V. Baker, Immunologic predictors of coronary artery calcium progression in a contemporary HIV cohort, AIDS, vol.28, issue.6, pp.831-840, 2014.
DOI : 10.1097/QAD.0000000000000145

A. Hasegawa, The level of monocyte turnover predicts disease progression in the macaque model of AIDS, Blood, vol.114, issue.14, pp.2917-2925, 2009.
DOI : 10.1182/blood-2009-02-204263

T. H. Burdo, Increased Monocyte Turnover from Bone Marrow Correlates with Severity of SIV Encephalitis and CD163 Levels in Plasma, PLoS Pathogens, vol.75, issue.4, p.1000842, 2010.
DOI : 10.1371/journal.ppat.1000842.t002

K. D. Mir, Simian Immunodeficiency Virus-Induced Alterations in Monocyte Production of Tumor Necrosis Factor Alpha Contribute to Reduced Immune Activation in Sooty Mangabeys, Journal of Virology, vol.86, issue.14, pp.7605-7615, 2012.
DOI : 10.1128/JVI.06813-11

D. Ma, SIVagm Infection in Wild African Green Monkeys from South Africa: Epidemiology, Natural History, and Evolutionary Considerations, PLoS Pathogens, vol.17, issue.1, p.1003011, 2013.
DOI : 10.1371/journal.ppat.1003011.s008

URL : http://doi.org/10.1371/journal.ppat.1003011

V. Wijewardana, Kinetics of Myeloid Dendritic Cell Trafficking and Activation: Impact on Progressive, Nonprogressive and Controlled SIV Infections, PLoS Pathogens, vol.38, issue.10, p.1003600, 2013.
DOI : 10.1371/journal.ppat.1003600.s009

S. P. Jochems, ABSTRACT, Journal of Virology, vol.89, issue.1, pp.751-762, 2015.
DOI : 10.1128/JVI.02430-14

T. Bruel, Plasmacytoid Dendritic Cell Dynamics Tune Interferon-Alfa Production in SIV-Infected Cynomolgus Macaques, PLoS Pathogens, vol.6, issue.7, p.1003915, 2014.
DOI : 10.1371/journal.ppat.1003915.s008

K. N. Brown, V. Wijewardana, X. Liu, and S. M. Barratt-boyes, Rapid Influx and Death of Plasmacytoid Dendritic Cells in Lymph Nodes Mediate Depletion in Acute Simian Immunodeficiency Virus Infection, PLoS Pathogens, vol.147, issue.5, p.1000413, 2009.
DOI : 10.1371/journal.ppat.1000413.s002

H. Donaghy, B. Gazzard, F. Gotch, and S. Patterson, Dysfunction and infection of freshly isolated blood myeloid and plasmacytoid dendritic cells in patients infected with HIV-1, Blood, vol.101, issue.11
DOI : 10.1182/blood-2002-10-3189

S. P. Jochems, ABSTRACT, Journal of Virology, vol.89, issue.13, pp.6918-6927, 2015.
DOI : 10.1128/JVI.00332-15

B. Jacquelin, Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response, Journal of Clinical Investigation, vol.119, pp.3544-3555, 2009.
DOI : 10.1172/JCI40093DS1

S. E. Bosinger, Intact Type I Interferon Production and IRF7 Function in Sooty Mangabeys, PLoS Pathogens, vol.1, issue.8, p.1003597, 2013.
DOI : 10.1371/journal.ppat.1003597.s007

O. M. Diop, Plasmacytoid Dendritic Cell Dynamics and Alpha Interferon Production during Simian Immunodeficiency Virus Infection with a Nonpathogenic Outcome, Journal of Virology, vol.82, issue.11
DOI : 10.1128/JVI.02433-07

URL : https://hal.archives-ouvertes.fr/hal-00345347

B. Jacquelin, Innate Immune Responses and Rapid Control of Inflammation in African Green Monkeys Treated or Not with Interferon-Alpha during Primary SIVagm Infection, PLoS Pathogens, vol.26, issue.7
DOI : 10.1371/journal.ppat.1004241.s005

N. G. Sandler, Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression, Nature, vol.37, issue.7511, pp.601-605, 2014.
DOI : 10.1182/blood-2012-06-437608

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418221

S. E. Bosinger, Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys, Journal of Clinical Investigation, vol.119, pp.3556-3572, 2009.
DOI : 10.1172/JCI40115DS1

O. Manches and N. Bhardwaj, Resolution of immune activation defines nonpathogenic SIV infection, Journal of Clinical Investigation, vol.119, pp.3512-3515, 2009.
DOI : 10.1172/JCI41509

N. Laguette, SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx, Nature, vol.38, issue.7353, pp.654-657, 2011.
DOI : 10.1038/nature10117

URL : https://hal.archives-ouvertes.fr/hal-00616451

J. Fonteneau, Human Immunodeficiency Virus Type 1 Activates Plasmacytoid Dendritic Cells and Concomitantly Induces the Bystander Maturation of Myeloid Dendritic Cells, Journal of Virology, vol.78, issue.10, pp.5223-5232, 2004.
DOI : 10.1128/JVI.78.10.5223-5232.2004

G. Eberl, M. Colonna, D. Santo, J. P. Mckenzie, and A. N. , Innate lymphoid cells: A new paradigm in immunology, Science, vol.348, issue.6237, pp.6566-6566, 2015.
DOI : 10.1126/science.aaa6566

URL : https://hal.archives-ouvertes.fr/pasteur-01402704

Q. Yang and A. Bhandoola, The development of adult innate lymphoid cells. Current Opinion in Immunology39, pp.114-120, 2016.

J. A. Walker, J. L. Barlow, and A. N. Mckenzie, Innate lymphoid cells ??? how did we miss them?, Nature Reviews Immunology, vol.186, issue.2, pp.75-87, 2013.
DOI : 10.1038/nri3349

T. Németh and A. Mócsai, Feedback Amplification of Neutrophil Function, Trends in Immunology, vol.37, issue.6, 2016.
DOI : 10.1016/j.it.2016.04.002

C. Tecchio and M. A. Cassatella, Neutrophil-derived chemokines on the road to immunity, Seminars in Immunology, vol.28, issue.2, 2016.
DOI : 10.1016/j.smim.2016.04.003

C. Elbim, The role of phagocytes in HIV-related oxidative stress, Journal of Clinical Virology, vol.20, issue.3, pp.99-109, 2001.
DOI : 10.1016/S1386-6532(00)00133-5

S. Casulli and C. Elbim, Interactions between Human Immunodeficiency Virus Type 1 and Polymorphonuclear Neutrophils, Journal of Innate Immunity, vol.6, issue.1, pp.13-20, 2014.
DOI : 10.1159/000353588

C. Elbim, P. D. Katsikis, and J. Estaquier, Neutrophil Apoptosis During Viral Infections, The Open Virology Journal, vol.3, issue.1, pp.52-59, 2009.
DOI : 10.2174/1874357900903010052

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703832

C. Elbim, Early Divergence in Neutrophil Apoptosis between Pathogenic and Nonpathogenic Simian Immunodeficiency Virus Infections of Nonhuman Primates, The Journal of Immunology, vol.181, issue.12
DOI : 10.4049/jimmunol.181.12.8613

C. Elbim, Increased neutrophil apoptosis in chronically SIV-infected macaques, Retrovirology, vol.6, issue.1, p.29, 2009.
DOI : 10.1186/1742-4690-6-29

URL : http://doi.org/10.1186/1742-4690-6-29

K. Amano, Neutrophils Induced Licensing of Natural Killer Cells, Mediators of Inflammation, vol.53, issue.2, p.747680, 2015.
DOI : 10.1007/s00262-013-1479-6

C. Costantini and M. A. Cassatella, The defensive alliance between neutrophils and NK cells as a novel arm of innate immunity, Journal of Leukocyte Biology, vol.89, issue.2, pp.221-233, 2011.
DOI : 10.1189/jlb.0510250

B. N. Jaeger, Neutrophil depletion impairs natural killer cell maturation, function, and homeostasis, The Journal of Experimental Medicine, vol.90, issue.3, pp.565-580, 2012.
DOI : 10.1016/j.immuni.2009.09.016

URL : https://hal.archives-ouvertes.fr/hal-00685480

K. Bandyopadhyay, I. Marrero, and V. Kumar, NKT cell subsets as key participants in liver physiology and pathology, Cellular & Molecular Immunology, vol.13, issue.3, pp.337-346, 2016.
DOI : 10.1002/hep.27791

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856801

L. Gapin, Development of invariant natural killer T cells, Current Opinion in Immunology, vol.39, pp.68-74, 2016.
DOI : 10.1016/j.coi.2016.01.001

J. L. Matsuda, Natural killer T cells reactive to a single glycolipid exhibit a highly diverse T cell receptor beta repertoire and small clone size, Proc. Natl. Acad. Sci
DOI : 10.1073/pnas.221445298

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC60106

P. T. Lee, K. Benlagha, L. Teyton, and A. Bendelac, Distinct Functional Lineages of Human V??24 Natural Killer T Cells, The Journal of Experimental Medicine, vol.195, issue.5, pp.637-641, 2002.
DOI : 10.1002/(SICI)1521-4141(199906)29:06<2014::AID-IMMU2014>3.0.CO;2-G

T. Takahashi, Cutting Edge: Analysis of Human V??24+CD8+ NK T Cells Activated by ??-Galactosylceramide-Pulsed Monocyte-Derived Dendritic Cells, The Journal of Immunology, vol.168, issue.7
DOI : 10.4049/jimmunol.168.7.3140

S. Ishihara, CD8+NKR-P1A+ T cells preferentially accumulate in human liver, European Journal of Immunology, vol.60, issue.8, pp.2406-2413, 1999.
DOI : 10.1002/(SICI)1521-4141(199908)29:08<2406::AID-IMMU2406>3.0.CO;2-F

C. S. Fernandez, Peripheral NKT Cells in Simian Immunodeficiency Virus-Infected Macaques, Journal of Virology, vol.83, issue.4, pp.1617-1624, 2009.
DOI : 10.1128/JVI.02138-08

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643790

N. Rout, Paucity of CD4+ Natural Killer T (NKT) Lymphocytes in Sooty Mangabeys Is Associated with Lack of NKT Cell Depletion after SIV Infection, PLoS ONE, vol.5, issue.3, p.9787, 2010.
DOI : 10.1371/journal.pone.0009787.t002

N. Rout, Loss of Effector and Anti-Inflammatory Natural Killer T Lymphocyte Function in Pathogenic Simian Immunodeficiency Virus Infection, PLoS Pathogens, vol.8, issue.9, p.1002928, 2012.
DOI : 10.1371/journal.ppat.1002928.t002

L. Campillo-gimenez, AIDS Progression Is Associated with the Emergence of IL-17-Producing Cells Early After Simian Immunodeficiency Virus Infection, The Journal of Immunology, vol.184, issue.2, pp.984-992, 2010.
DOI : 10.4049/jimmunol.0902316

URL : https://hal.archives-ouvertes.fr/hal-00456459

T. Hirai, Expansion of Regulatory T Cells, American Journal of Transplantation, vol.115, issue.2, pp.426-439, 2016.
DOI : 10.1111/ajt.13493

R. K. Reeves, Antigen-specific NK cell memory in rhesus macaques, Nature Immunology, vol.161, issue.9, pp.927-932, 2015.
DOI : 10.1186/1471-2164-12-295

J. L. Schafer, H. Li, T. I. Evans, J. D. Estes, and R. K. Reeves, ABSTRACT, Journal of Virology, vol.89, issue.13, pp.6887-6894, 2015.
DOI : 10.1128/JVI.00660-15

L. E. Pereira, R. P. Johnson, and A. A. Ansari, Sooty mangabeys and rhesus macaques exhibit significant divergent natural killer cell responses during both acute and chronic phases of SIV infection, Cellular Immunology, vol.254, issue.1, pp.10-19, 2008.
DOI : 10.1016/j.cellimm.2008.06.006

A. R. Stacey, 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, Journal of Virology, vol.83, issue.8, pp.3719-3733, 2009.
DOI : 10.1128/JVI.01844-08

Y. M. Mueller and P. Katsikis, IL-15 in HIV infection: pathogenic or therapeutic potential? Eur, Cytokine Netw, vol.21, pp.219-221, 2010.

N. Baumgarth, The double life of a B-1 cell: self-reactivity selects for protective effector functions, Nature Reviews Immunology, vol.237, issue.1, pp.34-46, 2011.
DOI : 10.1038/nri2901

D. Mucida, Transcriptional reprogramming of mature CD4+ helper T cells generates distinct MHC class II???restricted cytotoxic T lymphocytes, Nature Immunology, vol.158, issue.3, pp.281-289, 2013.
DOI : 10.1016/S0022-1759(03)00265-5

W. C. Warren, ), Genome Research, vol.25, issue.12
DOI : 10.1101/gr.192922.115

S. E. Bosinger, B. Jacquelin, A. Benecke, G. Silvestri, and M. Müller-trutwin, Systems biology of natural simian immunodeficiency virus infections, Current Opinion in HIV and AIDS, vol.7, issue.1, pp.71-78, 2012.
DOI : 10.1097/COH.0b013e32834dde01

S. Galván-peña and L. A. Neill, Metabolic reprograming in macrophage polarization. Front Immunol5, p.420, 2014.

E. Kasmi, K. C. Stenmark, and K. R. , Contribution of metabolic reprogramming to macrophage plasticity and function, Seminars in Immunology, vol.27, issue.4, pp.267-275, 2015.
DOI : 10.1016/j.smim.2015.09.001

A. Saez-cirion, B. Jacquelin, F. Barré-sinoussi, and M. Müller-trutwin, Immune responses during spontaneous control of HIV and AIDS: what is the hope for a cure?, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.155, issue.4, p.20130436, 2014.
DOI : 10.1084/jem.20122824

URL : https://hal.archives-ouvertes.fr/pasteur-01420530