M. Negroni and H. Buc, Mechanisms of Retroviral Recombination, Annual Review of Genetics, vol.35, issue.1, pp.275-302, 2001.
DOI : 10.1146/annurev.genet.35.102401.090551

T. Schlub, A. Grimm, R. Smyth, D. Cromer, A. Chopra et al., Fifteen to Twenty Percent of HIV Substitution Mutations Are Associated with Recombination, Journal of Virology, vol.88, issue.7, pp.3837-384903136, 2014.
DOI : 10.1128/JVI.03136-13

B. Poiesz, F. Ruscetti, A. Gazdar, P. Bunn, J. Minna et al., Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma, Proceedings of the National Academy of Sciences, vol.77, issue.12, pp.7415-7419, 1980.
DOI : 10.1073/pnas.77.12.7415

E. Wattel, J. Vartanian, C. Pannetier, and S. Wain-hobson, Clonal expansion of human T-cell leukemia virus type I-infected cells in asymptomatic and symptomatic carriers without malignancy, J. Virol, vol.69, pp.2863-2868, 1995.

L. Cook, A. Rowan, A. Melamed, G. Taylor, and C. Bangham, HTLV-1-infected T cells contain a single integrated provirus in natural infection, Blood, vol.120, issue.17, pp.3488-3490, 2012.
DOI : 10.1182/blood-2012-07-445593

A. Gessain and O. Cassar, Epidemiological Aspects and World Distribution of HTLV-1 Infection, Frontiers in Microbiology, vol.3, p.388, 2012.
DOI : 10.3389/fmicb.2012.00388
URL : https://hal.archives-ouvertes.fr/pasteur-01370951

M. Yoshida, I. Miyoshi, and Y. Hinuma, Isolation and characterization of retrovirus from cell lines of human adult T-cell leukemia and its implication in the disease., Proceedings of the National Academy of Sciences, vol.79, issue.6, pp.2031-2035, 1982.
DOI : 10.1073/pnas.79.6.2031

A. Gessain, F. Barin, J. Vernant, O. Gout, L. Maurs et al., ANTIBODIES TO HUMAN T-LYMPHOTROPIC VIRUS TYPE-I IN PATIENTS WITH TROPICAL SPASTIC PARAPARESIS, The Lancet, vol.326, issue.8452, pp.407-410, 1985.
DOI : 10.1016/S0140-6736(85)92734-5

A. Gessain, R. Gallo, and G. Franchini, Low degree of human T-cell leukemia/lymphoma virus type I genetic drift in vivo as a means of monitoring viral transmission and movement of ancient human populations, J. Virol, vol.66, pp.2288-2295, 1992.

L. Alcantara, T. De-oliveira, M. Gordon, O. Pybus, R. Mascarenhas et al., Tracing the origin of Brazilian HTLV-1 as determined by analysis of host and viral genes, AIDS, vol.20, issue.5, pp.780-782, 2006.
DOI : 10.1097/01.aids.0000216383.14808.13

A. Mota, S. Van-dooren, F. Fernandes, S. Pereira, A. Queiroz et al., The Close Relationship between South African and Latin American HTLV Type 1 Strains Corroborated in a Molecular Epidemiological Study of the HTLV Type 1 Isolates from a Blood Donor Cohort, AIDS Research and Human Retroviruses, vol.23, issue.4, pp.503-507, 2007.
DOI : 10.1089/aid.2006.0203

O. Cassar, L. Einsiedel, P. Afonso, and A. Gessain, Human T-Cell Lymphotropic Virus Type 1 Subtype C Molecular Variants among Indigenous Australians: New Insights into the Molecular Epidemiology of HTLV-1 in Australo-Melanesia, PLoS Neglected Tropical Diseases, vol.2, issue.9, 2013.
DOI : 10.1371/journal.pntd.0002418.t002
URL : https://hal.archives-ouvertes.fr/pasteur-01370943

L. Meertens, J. Rigoulet, P. Mauclere, M. Van-beveren, G. Chen et al., Molecular and Phylogenetic Analyses of 16 Novel Simian T Cell Leukemia Virus Type 1 from Africa: Close Relationship of STLV-1 from Allenopithecus nigroviridis to HTLV-1 Subtype B Strains, Virology, vol.287, issue.2, pp.275-285, 1018.
DOI : 10.1006/viro.2001.1018

X. Xia, DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution, Molecular Biology and Evolution, vol.30, issue.7, pp.1720-1728, 2013.
DOI : 10.1093/molbev/mst064

D. Posada and K. Crandall, MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, issue.9, pp.817-818, 1998.
DOI : 10.1093/bioinformatics/14.9.817

K. Lole, R. Bollinger, R. Paranjape, D. Gadkari, S. Kulkarni et al., Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination, J. Virol, vol.73, pp.152-160, 1999.

K. Nieselt-struwe, V. Haeseler, and A. , Quartet-Mapping, a Generalization of the Likelihood-Mapping Procedure, Molecular Biology and Evolution, vol.18, issue.7, pp.1204-1219, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003907

M. Salemi, J. Desmyter, and A. Vandamme, Tempo and Mode of Human and Simian T-Lymphotropic Virus (HTLV/STLV) Evolution Revealed by Analyses of Full-Genome Sequences, Molecular Biology and Evolution, vol.17, issue.3, pp.374-386, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026317

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

R. Mahieux, F. Ibrahim, P. Mauclere, V. Herve, P. Michel et al., Molecular epidemiology of 58 new African human T-cell leukemia virus type 1 (HTLV-1) strains: identification of a new and distinct HTLV-1 molecular subtype in Central Africa and in pygmies, J. Virol, vol.71, pp.1317-1333, 1997.

M. Salemi, S. Van-dooren, E. Audenaert, E. Delaporte, P. Goubau et al., Two New Human T-Lymphotropic Virus Type I Phylogenetic Subtypes in Seroindeterminates, a Mbuti Pygmy and a Gabonese, Have Closest Relatives among African STLV-I Strains, Virology, vol.246, issue.2, pp.277-287, 1998.
DOI : 10.1006/viro.1998.9215

J. Slattery, G. Franchini, and A. Gessain, Genomic evolution, patterns of global dissemination, and interspecies transmission of human and simian T-cell leukemia/lymphotropic viruses, Genome Res, vol.9, pp.525-540, 1999.

C. Van-tienen, T. De-silva, L. Alcantara, C. Onyango, S. Jarju et al., Molecular Epidemiology of Endemic Human T-Lymphotropic Virus Type 1 in a Rural Community in Guinea-Bissau, PLoS Neglected Tropical Diseases, vol.203, issue.6, p.1690, 2012.
DOI : 10.1371/journal.pntd.0001690.s001

G. Zehender, E. Ebranati, D. Maddalena, C. Gianelli, E. Riva et al., Description of a ???Trans-Saharan??? Strain of Human T-Lymphotropic Virus Type 1 in West Africa, JAIDS Journal of Acquired Immune Deficiency Syndromes, vol.47, issue.3, pp.269-273, 2008.
DOI : 10.1097/QAI.0b013e31816649a4

W. Hu and S. Hughes, HIV-1 reverse transcription. Cold Spring Harb, 2012.

D. Robertson, P. Sharp, F. Mccutchan, and B. Hahn, Recombination in HIV-1, Nature, vol.374, issue.6518, pp.124-126, 1995.
DOI : 10.1038/374124b0

L. Cook, A. Melamed, H. Niederer, M. Valganon, D. Laydon et al., The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemia/lymphoma, Blood, vol.123, issue.25, 2014.
DOI : 10.1182/blood-2014-02-553602

C. Bangham, L. Cook, and A. Melamed, HTLV-1 clonality in adult T-cell leukaemia and non-malignant HTLV-1 infection, Seminars in Cancer Biology, vol.26, pp.89-98, 2013.
DOI : 10.1016/j.semcancer.2013.11.003

P. Jain, S. Manuel, Z. Khan, J. Ahuja, K. Quann et al., DC-SIGN Mediates Cell-Free Infection and Transmission of Human T-Cell Lymphotropic Virus Type 1 by Dendritic Cells, Journal of Virology, vol.83, issue.21, pp.10908-1092101054, 2009.
DOI : 10.1128/JVI.01054-09

K. Jones, C. Petrow-sadowski, Y. Huang, D. Bertolette, and F. Ruscetti, Cell-free HTLV-1 infects dendritic cells leading to transmission and transformation of CD4+ T cells, Nature Medicine, vol.174, issue.4, pp.429-436, 2008.
DOI : 10.1182/blood.V99.1.88