J. Blankson, D. Persaud, and R. Siliciano, The Challenge of Viral Reservoirs in HIV-1 Infection, Annual Review of Medicine, vol.53, issue.1, pp.557-593, 2002.
DOI : 10.1146/annurev.med.53.082901.104024

S. Eriksson, E. Graf, V. Dahl, M. Strain, and S. Yukl, Comparative Analysis of Measures of Viral Reservoirs in HIV-1 Eradication Studies, PLoS Pathogens, vol.108, issue.2, 2013.
DOI : 10.1371/journal.ppat.1003174.t004

C. Goujard, M. Bonarek, L. Meyer, F. Bonnet, and M. Chaix, 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.709-715, 2006.
DOI : 10.1086/500213

M. Cohen, G. Shaw, and A. Mcmichael, Acute HIV-1 Infection, New England Journal of Medicine, vol.364, issue.20, pp.1943-1954
DOI : 10.1056/NEJMra1011874

B. Keele, E. Giorgi, J. Salazar-gonzalez, J. Decker, and K. Pham, Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection, Proceedings of the National Academy of Sciences, vol.79, issue.16, pp.7552-7557, 2008.
DOI : 10.1128/JVI.79.16.10108-10125.2005

A. Mcmichael, P. Borrow, G. Tomaras, N. Goonetilleke, and B. Haynes, The immune response during acute HIV-1 infection: clues for vaccine development, Nature Reviews Immunology, vol.9, issue.1, pp.11-23
DOI : 10.1038/nri2674

J. Mattapallil, D. Douek, B. Hill, Y. Nishimura, and M. Martin, Massive infection and loss of memory CD4+ T cells in multiple tissues during acute SIV infection, Nature, vol.82, issue.7037, pp.1093-1097, 2005.
DOI : 10.1084/jem.164.1.280

S. Kinloch-de-loes, P. De-saussure, J. Saurat, H. Stalder, and B. Hirschel, Symptomatic Primary Infection Due to Human Immunodeficiency Virus Type 1: Review of 31 Cases, Clinical Infectious Diseases, vol.17, issue.1, pp.59-65, 1993.
DOI : 10.1093/clinids/17.1.59

L. Roberts, J. Passmore, C. Williamson, F. Little, and L. Bebell, Plasma cytokine levels during acute HIV-1 infection predict HIV disease progression, AIDS, vol.24, issue.6, pp.819-831
DOI : 10.1097/QAD.0b013e3283367836

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001189

T. Chun, L. Carruth, D. Finzi, X. Shen, and J. Digiuseppe, Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection, Nature, vol.387, issue.6629, pp.183-188, 1997.
DOI : 10.1038/387183a0

T. Chun, J. Justement, D. Murray, C. Hallahan, and J. Maenza, Rebound of plasma viremia following cessation of antiretroviral therapy despite profoundly low levels of HIV reservoir: implications for eradication, AIDS, vol.24, issue.18
DOI : 10.1097/QAD.0b013e328340a239

T. Schacker, S. Little, E. Connick, K. Gebhard, and Z. Zhang, Productive Infection of T Cells in Lymphoid Tissues during Primary and Early Human Immunodeficiency Virus Infection, The Journal of Infectious Diseases, vol.183, issue.4, pp.555-562, 2001.
DOI : 10.1086/318524

T. Chun, D. Engel, M. Berrey, T. Shea, and L. Corey, Early establishment of a pool of latently infected, resting CD4+ T cells during primary HIV-1 infection, Proceedings of the National Academy of Sciences, vol.32, issue.3, pp.8869-8873, 1998.
DOI : 10.1146/annurev.iy.13.040195.002415

E. Fiebig, D. Wright, B. Rawal, P. Garrett, and R. Schumacher, Dynamics of HIV viremia and antibody seroconversion in plasma donors, AIDS, vol.17, issue.13, pp.1871-1879, 2003.
DOI : 10.1097/00002030-200309050-00005

J. Ananworanich, A. Schuetz, C. Vandergeeten, I. Sereti, and M. De-souza, Impact of Multi-Targeted Antiretroviral Treatment on Gut T Cell Depletion and HIV Reservoir Seeding during Acute HIV Infection, PLoS ONE, vol.355, issue.3, p.33948
DOI : 10.1371/journal.pone.0033948.t002

M. Centlivre, N. Legrand, R. Steingrover, R. Van-der-sluis, and M. Grijsen, Altered dynamics and differential infection profiles of lymphoid and myeloid cell subsets during acute and chronic HIV-1 infection, Journal of Leukocyte Biology, vol.89, issue.5
DOI : 10.1189/jlb.0410231

A. Ganesan, P. Chattopadhyay, T. Brodie, J. Qin, and W. Gu, Immunologic and Virologic Events in Early HIV Infection Predict Subsequent Rate of Progression, The Journal of Infectious Diseases, vol.201, issue.2, pp.272-284
DOI : 10.1086/649430

C. Dalmasso, W. Carpentier, L. Meyer, C. Rouzioux, and C. Goujard, Distinct Genetic Loci Control Plasma HIV-RNA and Cellular HIV-DNA Levels in HIV-1 Infection: The ANRS Genome Wide Association 01 Study, PLoS ONE, vol.46, issue.12, p.3907, 2008.
DOI : 10.1371/journal.pone.0003907.s002

L. Josefsson, M. King, B. Makitalo, J. Brannstrom, and W. Shao, Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule, Proceedings of the National Academy of Sciences, vol.22, issue.4, pp.11199-11204
DOI : 10.1128/JCM.43.1.406-413.2005

M. Stevenson, T. Stanwick, M. Dempsey, and C. Lamonica, HIV-1 replication is controlled at the level of T cell activation and proviral integration, The EMBO journal, vol.9, pp.1551-1560, 1990.

C. Goujard, M. Bonarek, L. Meyer, F. Bonnet, and M. Chaix, 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 : an official publication of the Infectious Diseases Society, America, vol.42, pp.709-715, 2006.

R. Siliciano, HIV Eradication: Understanding the magnitude of the problem. Presented at the International AIDS Society's Pre-Conference Symposium ''Towards an HIV Cure, 2012.

M. Cohen, C. Gay, and M. Busch, The Detection of Acute HIV Infection, The Journal of Infectious Diseases, vol.202, issue.S2, pp.270-277
DOI : 10.1086/655651

N. Chomont, H. Hocini, G. Gresenguet, C. Brochier, and H. Bouhlal, Early archives of genetically-restricted proviral DNA in the female genital tract after heterosexual transmission of HIV-1, AIDS, vol.21, issue.2, pp.153-162, 2007.
DOI : 10.1097/QAD.0b013e328011f94b

V. Avettand-fenoel, L. Hocqueloux, M. Muller-trutwin, T. Prazuck, and A. Melard, Greater diversity of HIV DNA variants in the rectum compared to variants in the blood in patients without HAART, Journal of Medical Virology, vol.70, issue.9, pp.1499-1507
DOI : 10.1002/jmv.22132

URL : https://hal.archives-ouvertes.fr/hal-00657572

P. Benaroch, E. Billard, R. Gaudin, and M. Schindler, HIV-1 assembly in macrophages, Retrovirology, vol.7, issue.1, p.29
DOI : 10.1186/1742-4690-7-29

URL : https://hal.archives-ouvertes.fr/inserm-00663901

H. Blaak, A. Van-'t-wout, M. Brouwer, B. Hooibrink, and E. Hovenkamp, In vivo HIV-1 infection of CD45RA+CD4+ T cells is established primarily by syncytium-inducing variants and correlates with the rate of CD4+ T cell decline, Proceedings of the National Academy of Sciences, vol.72, issue.12, pp.1269-1274, 2000.
DOI : 10.1126/science.1925601

N. Chomont, M. El-far, P. Ancuta, L. Trautmann, and F. Procopio, HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation, Nature Medicine, vol.45, issue.8, 2009.
DOI : 10.1038/nm.1972

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859814

E. Managlia, A. Landay, and L. Harthi, Interleukin-7 induces HIV replication in primary naive T cells through a nuclear factor of activated T cell (NFAT)-dependent pathway, Virology, vol.350, issue.2, pp.443-452, 2006.
DOI : 10.1016/j.virol.2006.02.019

L. Pedroza-martins, W. Boscardin, D. Anisman-posner, D. Schols, and Y. Bryson, Impact of Cytokines on Replication in the Thymus of Primary Human Immunodeficiency Virus Type 1 Isolates from Infants, Journal of Virology, vol.76, issue.14, pp.6929-6943, 2002.
DOI : 10.1128/JVI.76.14.6929-6943.2002

C. Pilcher, J. Eron, S. Galvin, C. Gay, and M. Cohen, Acute HIV revisited: new opportunities for treatment and prevention, Journal of Clinical Investigation, vol.116, issue.12, pp.937-945, 2004.
DOI : 10.1172/JCI21540C1

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1679701

V. Avettand-fenoel, M. Chaix, S. Blanche, M. Burgard, and C. Floch, LTR real-time PCR for HIV-1 DNA quantitation in blood cells for early diagnosis in infants born to seropositive mothers treated in HAART area (ANRS CO 01), J Med Virol, vol.81, pp.217-223, 2009.

E. Delwart, E. Shpaer, J. Louwagie, F. Mccutchan, and M. Grez, Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes, Science, vol.262, issue.5137, pp.1257-1261, 1993.
DOI : 10.1126/science.8235655

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980.
DOI : 10.1007/BF01731581