M. Thomson, L. Pérez-alvarez, and R. Nájera, Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy, The Lancet Infectious Diseases, vol.2, issue.8, pp.461-71, 2002.
DOI : 10.1016/S1473-3099(02)00343-2

M. Peeters, A. Aghokeng, and E. Delaporte, Genetic diversity among human immunodeficiency virus-1 non-B subtypes in viral load and drug resistance assays, Clinical Microbiology and Infection, vol.16, issue.10, pp.1525-1556, 2010.
DOI : 10.1111/j.1469-0691.2010.03300.x

L. Gamble and Q. Matthews, Current progress in the development of a prophylactic vaccine for HIV-1, Drug Des Devel Ther Review, vol.5, pp.9-26, 2010.

D. Tebit and E. Arts, Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease, The Lancet Infectious Diseases, vol.11, issue.1, pp.45-56, 2011.
DOI : 10.1016/S1473-3099(10)70186-9

N. Vidal, M. Peeters, C. Mulanga-kabeya, N. Nzilambi, and D. Robertson, Unprecedented Degree of Human Immunodeficiency Virus Type 1 (HIV-1) Group M Genetic Diversity in the Democratic Republic of Congo Suggests that the HIV-1 Pandemic Originated in Central Africa, Journal of Virology, vol.74, issue.22, pp.10498-507, 2000.
DOI : 10.1128/JVI.74.22.10498-10507.2000

A. Rambaut, D. Robertson, O. Pybus, M. Peeters, and E. Holmes, Human immunodeficiency virus. Phylogeny and the origin of HIV-1, Nature, vol.410, issue.6832, pp.1047-1055, 2001.
DOI : 10.1038/35074179

M. Worobey, M. Gemmel, D. Teuwen, T. Haselkorn, and K. Kunstman, Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960, Nature, vol.54, issue.7213, pp.661-665, 2008.
DOI : 10.1038/nature07390

J. Hemelaar, E. Gouws, P. Ghys, S. Osmanov, and . Who-unaids, Global trends in molecular epidemiology of HIV-1 during 2000???2007, AIDS, vol.25, issue.5, pp.679-89, 2000.
DOI : 10.1097/QAD.0b013e328342ff93

F. Barin, M. Boup, S. Denis, F. Kanki, P. Allan et al., SEROLOGICAL EVIDENCE FOR VIRUS RELATED TO SIMIAN T-LYMPHOTROPIC RETROVIRUS III IN RESIDENTS OF WEST AFRICA, The Lancet, vol.326, issue.8469-8470, pp.1387-1396, 1985.
DOI : 10.1016/S0140-6736(85)92556-5

D. Hamel, J. Sankalé, G. Eisen, S. Meloni, and C. Mullins, Twenty Years of Prospective Molecular Epidemiology in Senegal: Changes in HIV Diversity, AIDS Research and Human Retroviruses, vol.23, issue.10, pp.1189-96, 2007.
DOI : 10.1089/aid.2007.0037

U. Website, Available: www.unaids.org/en/regionscountries/countries/ senegal, 2011.

C. Toure-kane, C. Montavon, M. Faye, P. Gueye, and P. Sow, Sequence Note: Identification of All HIV Type 1 Group M Subtypes in Senegal, a Country with Low and Stable Seroprevalence, AIDS Research and Human Retroviruses, vol.16, issue.6, pp.603-612, 2000.
DOI : 10.1089/088922200309025

A. Ayouba, T. Lien, J. Nouhin, L. Vergne, and A. Aghokeng, Low Prevalence of HIV Type 1 Drug Resistance Mutations in Untreated, Recently Infected Patients from Burkina Faso, C??te d'Ivoire, Senegal, Thailand, and Vietnam: The ANRS 12134 Study, AIDS Research and Human Retroviruses, vol.25, issue.11, pp.1193-1199, 2009.
DOI : 10.1089/aid.2009.0142

H. Diop-ndiaye, C. Toure-kane, N. Leye, N. Ngom-gueye, and C. Montavon, Antiretroviral Drug Resistance Mutations in Antiretroviral-Naive Patients from Senegal, AIDS Research and Human Retroviruses, vol.26, issue.10, pp.1133-1141, 2010.
DOI : 10.1089/aid.2009.0295

H. Ndiaye, C. Toure-kane, N. Vidal, F. Niama, and P. Niang-diallo, Surprisingly High Prevalence of Subtype C and Specific HIV-1 Subtype/CRF Distribution in Men Having Sex With Men in Senegal, JAIDS Journal of Acquired Immune Deficiency Syndromes, vol.52, issue.2, pp.249-52, 2009.
DOI : 10.1097/QAI.0b013e3181af70a4

E. Soares, A. Martinez, T. Souza, A. Santos, D. Hora et al., HIV-1 subtype C dissemination in southern Brazil, AIDS, vol.19, issue.Suppl 4, 2005.
DOI : 10.1097/01.aids.0000191497.00928.e4

A. Wade, C. Kane, P. Diallo, A. Diop, and K. Gueye, HIV infection and sexually transmitted infections among men who have sex with men in Senegal, AIDS, vol.19, issue.18, pp.2133-2140, 2005.
DOI : 10.1097/01.aids.0000194128.97640.07

M. Thomson and A. Fernández-garcía, Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning, Virology, vol.415, issue.1, pp.30-38, 2011.
DOI : 10.1016/j.virol.2011.03.021

R. Fontella, M. Soares, and C. Schrago, On the origin of HIV-1 subtype C in South America, AIDS, vol.22, issue.15, pp.2001-2012, 2008.
DOI : 10.1097/QAD.0b013e3283108f69

G. Bello, C. Passaes, M. Guimarães, R. Lorete, M. Almeida et al., Origin and evolutionary history of HIV-1 subtype C in Brazil, AIDS, vol.22, issue.15, pp.1993-2000, 2008.
DOI : 10.1097/QAD.0b013e328315e0aa

T. De-oliveira, D. Pillay, and R. Gifford, The HIV-1 Subtype C Epidemic in South America Is Linked to the United Kingdom, PLoS ONE, vol.6, issue.2, p.9311
DOI : 10.1371/journal.pone.0009311.s004

N. Véras, R. Gray, L. Brígido, R. Rodrigues, and M. Salemi, High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America, Journal of General Virology, vol.92, issue.7, pp.1698-709, 2011.
DOI : 10.1099/vir.0.028951-0

F. Kane, M. Alary, I. Ndoye, A. Coll, and S. , Temporary expatriation is related to HIV-1 infection in rural Senegal, AIDS, vol.7, issue.9, pp.1261-1266, 1993.
DOI : 10.1097/00002030-199309000-00017

P. Kanki, M. Peeters, and A. Gueye-ndiaye, Virology of HIV-1 and HIV-2: implications for Africa, AIDS, vol.11, pp.33-37, 1997.

P. Kanki, D. Hamel, J. Sankalé, C. Hsieh, and I. Thior, Human Immunodeficiency Virus Type 1 Subtypes Differ in Disease Progression, The Journal of Infectious Diseases, vol.179, issue.1, pp.68-73, 1999.
DOI : 10.1086/314557

D. Tully and C. Wood, Chronology and evolution of the HIV-1 subtype C epidemic in Ethiopia, AIDS, vol.24, issue.10, pp.1577-82, 2010.
DOI : 10.1097/QAD.0b013e32833999e1

S. Dalai, T. De-oliveira, G. Harkins, S. Kassaye, and J. Lint, Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe, AIDS, vol.23, issue.18, pp.2523-2555, 2009.
DOI : 10.1097/QAD.0b013e3283320ef3

S. Travers, J. Clewley, J. Glynn, P. Fine, and A. Crampin, Timing and Reconstruction of the Most Recent Common Ancestor of the Subtype C Clade of Human Immunodeficiency Virus Type 1, Journal of Virology, vol.78, issue.19, pp.10501-10507, 2004.
DOI : 10.1128/JVI.78.19.10501-10506.2004

L. Mcdaid and G. Hart, Sexual risk behaviour for transmission of HIV in men who have sex with men: recent findings and potential interventions, Current Opinion in HIV and AIDS, vol.5, issue.4, pp.311-316, 2010.
DOI : 10.1097/COH.0b013e32833a0b86

A. Abraha, I. Nankya, R. Gibson, K. Demers, and D. Tebit, CCR5- and CXCR4-Tropic Subtype C Human Immunodeficiency Virus Type 1 Isolates Have a Lower Level of Pathogenic Fitness than Other Dominant Group M Subtypes: Implications for the Epidemic, Journal of Virology, vol.83, issue.11, pp.5592-5605, 2009.
DOI : 10.1128/JVI.02051-08

S. Ball, A. Abraha, K. Collins, A. Marozsan, and H. Baird, Comparing the Ex Vivo Fitness of CCR5-Tropic Human Immunodeficiency Virus Type 1 Isolates of Subtypes B and C, Journal of Virology, vol.77, issue.2, pp.1021-1059, 2003.
DOI : 10.1128/JVI.77.2.1021-1038.2003

B. Renjifo, P. Gilbert, B. Chaplin, G. Msamanga, and D. Mwakagile, Preferential in-utero transmission of HIV-1 subtype C as compared to HIV-1 subtype A or D, AIDS, vol.18, issue.12, pp.1629-1636, 2004.
DOI : 10.1097/01.aids.0000131392.68597.34

G. John-stewart, R. Nduati, C. Rousseau, D. Mbori-ngacha, and B. Richardson, Subtype C Is Associated with Increased Vaginal Shedding of HIV???1, The Journal of Infectious Diseases, vol.192, issue.3, pp.492-496, 2005.
DOI : 10.1086/431514

J. Martinez-cajas, N. Pai, M. Klein, and M. Wainberg, Differences in resistance mutations among HIV-1 non-subtype B infections: a systematic review of evidence (1996???2008), Journal of the International AIDS Society, vol.12, issue.1, p.11, 1996.
DOI : 10.1186/1758-2652-12-11

L. Vergne, J. Snoeck, A. Aghokeng, B. Maes, and D. Valea, Genotypic drug resistance interpretation algorithms display high levels of discordance when applied to non-B strains from HIV-1 naive and treated patients, FEMS Immunology & Medical Microbiology, vol.46, issue.1, pp.53-62, 2006.
DOI : 10.1111/j.1574-695X.2005.00011.x

J. Snoeck, R. Kantor, R. Shafer, K. Van-laethem, and K. Deforche, Discordances between Interpretation Algorithms for Genotypic Resistance to Protease and Reverse Transcriptase Inhibitors of Human Immunodeficiency Virus Are Subtype Dependent, Antimicrobial Agents and Chemotherapy, vol.50, issue.2, pp.694-701, 2006.
DOI : 10.1128/AAC.50.2.694-701.2006

J. Neilson, G. John, J. Carr, P. Lewis, and J. Kreiss, Subtypes of human immunodeficiency virus type 1 and disease stage among women in Nairobi, Kenya, J Virol, vol.73, pp.4393-4403, 1999.

D. Bennett, S. Bertagnolio, D. Sutherland, and C. Gilks, The World Health Organization's global strategy for prevention and assessment of HIV drug resistance, Antivir Ther, vol.13, issue.2, pp.1-13, 2008.

T. De-oliveira, K. Deforche, S. Cassol, M. Salminen, and D. Paraskevis, An automated genotyping system for analysis of HIV-1 and other microbial sequences, Bioinformatics, vol.21, issue.19, pp.3797-800, 2005.
DOI : 10.1093/bioinformatics/bti607

L. Alcantara, S. Cassol, P. Libin, K. Deforche, and O. Pybus, A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences, Nucleic Acids Research, vol.37, issue.Web Server, pp.634-676, 2009.
DOI : 10.1093/nar/gkp455

L. Vergne, S. Diagbouga, C. Kouanfack, A. Aghokeng, and C. Butel, HIV- 1 drug-resistance mutations among newly diagnosed patients before scaling-up programmes in Burkina Faso and Cameroon, Antivir Ther, vol.11, pp.575-584, 2006.

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-3066, 2002.
DOI : 10.1093/nar/gkf436

K. Katoh, K. Kuma, H. Toh, and T. Miyata, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Research, vol.33, issue.2, pp.511-519, 2005.
DOI : 10.1093/nar/gki198

K. Tamura, D. Peterson, N. Peterson, G. Stecher, and M. Nei, MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2740, 2011.
DOI : 10.1093/molbev/msr121

D. Bennett, R. Camacho, D. Otelea, D. Kuritzkes, and H. Fleury, Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update, PLoS ONE, vol.81, issue.3, 2009.
DOI : 10.1371/journal.pone.0004724.t004

D. Posada and K. Crandall, Selecting Models of Nucleotide Substitution: An Application to Human Immunodeficiency Virus 1 (HIV-1), Molecular Biology and Evolution, vol.18, issue.6, pp.897-906, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003890

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, and W. Hordijk, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-328, 2010.
DOI : 10.1093/sysbio/syq010

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

M. Anisimova and O. Gascuel, Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative, Systematic Biology, vol.55, issue.4, pp.539-52, 2006.
DOI : 10.1080/10635150600755453

URL : https://hal.archives-ouvertes.fr/lirmm-00136658

F. Ronquist and J. Huelsenbeck, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, vol.19, issue.12, pp.1572-1574, 2003.
DOI : 10.1093/bioinformatics/btg180

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/19/12/1572

A. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, p.214, 2007.
DOI : 10.1186/1471-2148-7-214

A. Drummond, S. Ho, M. Phillips, and A. Rambaut, Relaxed Phylogenetics and Dating with Confidence, PLoS Biology, vol.20, issue.5, p.88, 2006.
DOI : 10.1371/journal.pbio.0040088.sd001

URL : http://doi.org/10.1371/journal.pbio.0040088

V. Minin, E. Bloomquist, and M. Suchard, Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics, Molecular Biology and Evolution, vol.25, issue.7, pp.1459-71, 2008.
DOI : 10.1093/molbev/msn090

B. Brown, J. Darden, S. Tovanabutra, T. Oblander, and J. Frost, Biologic and Genetic Characterization of a Panel of 60 Human Immunodeficiency Virus Type 1 Isolates, Representing Clades A, B, C, D, CRF01_AE, and CRF02_AG, for the Development and Assessment of Candidate Vaccines, Journal of Virology, vol.79, issue.10, pp.6089-101, 2005.
DOI : 10.1128/JVI.79.10.6089-6101.2005

L. Vergne, C. Kane, C. Laurent, N. Diakhaté, and N. Gueye, Low rate of genotypic HIV-1 drug-resistant strains in the Senegalese government initiative of access to antiretroviral therapy, AIDS, vol.17, issue.3, pp.31-39, 2003.
DOI : 10.1097/00002030-200317003-00005

L. Vergne, M. Peeters, E. Mpoudi-ngole, A. Bourgeois, and F. Liegeois, Genetic diversity of protease and reverse transcriptase sequences in non-subtype- B human immunodeficiency virus type 1 strains: evidence of many minor drug resistance mutations in treatment-na?¨vena?¨ve patients, J Clin Microbiol, vol.38, pp.3919-3944, 2000.