. Caen and A. Pr, Vabret); Clermont-Ferrand (Dr C. Henquell, Dr A. Mirand)

A. G. Paris-neckerdr, P. V. Marcelin, . Calvez, S. Dr, D. C. Lambert-niclot et al., Avettand-Fenoel); Paris-Pitié-Salpêtrière Wirden); Paris Saint-Antoine (Dr L. Morand-Joubert), Dr M.L. Chaix

J. Toulouse-(-pr, . Izopet, S. Dr, . Raymond, . Tours et al., Chaillon); Versailles (Dr S. Marque-Juillet); Villejuif (Pr A.M. Roque-Afonso, Dr S. Haïm-Boukobza), INSERM UMR-S1136 (Dr P. Flandre, M. Grudé, Dr L. Assoumou, Dr D. Costagliola). The lead author for the ANRS AC11 Study Group is Dr Diane Descamps

E. Berger, P. Murphy, and J. Farber, CHEMOKINE RECEPTORS AS HIV-1 CORECEPTORS: Roles in Viral Entry, Tropism, and Disease, Annual Review of Immunology, vol.17, issue.1, pp.657-700, 1999.
DOI : 10.1146/annurev.immunol.17.1.657

P. Dorr, M. Westby, S. Dobbs, P. Griffin, B. Irvine et al., Maraviroc (UK-427,857), a Potent, Orally Bioavailable, and Selective Small-Molecule Inhibitor of Chemokine Receptor CCR5 with Broad-Spectrum Anti-Human Immunodeficiency Virus Type 1 Activity, Antimicrobial Agents and Chemotherapy, vol.49, issue.11, pp.4721-4732, 2005.
DOI : 10.1128/AAC.49.11.4721-4732.2005

M. Westby, M. Lewis, J. Whitcomb, M. Youle, A. Pozniak et al., Emergence of CXCR4-Using Human Immunodeficiency Virus Type 1 (HIV-1) Variants in a Minority of HIV-1-Infected Patients following Treatment with the CCR5 Antagonist Maraviroc Is from a Pretreatment CXCR4-Using Virus Reservoir, Journal of Virology, vol.80, issue.10, pp.4909-4920, 2006.
DOI : 10.1128/JVI.80.10.4909-4920.2006

J. Whitcomb, W. Huang, S. Fransen, K. Limoli, J. Toma et al., Development and Characterization of a Novel Single-Cycle Recombinant-Virus Assay To Determine Human Immunodeficiency Virus Type 1 Coreceptor Tropism, Antimicrobial Agents and Chemotherapy, vol.51, issue.2, pp.566-575, 2007.
DOI : 10.1128/AAC.00853-06

J. Rose, A. Rhea, J. Weber, and M. Quinones-mateu, Current tests to evaluate HIV-1 coreceptor tropism, Current Opinion in HIV and AIDS, vol.4, issue.2, pp.136-142, 2009.
DOI : 10.1097/COH.0b013e328322f973

S. Raymond, P. Delobel, M. Mavigner, M. Cazabat, C. Souyris et al., Correlation between genotypic predictions based on V3 sequences and phenotypic determination of HIV-1 tropism, AIDS, vol.22, issue.14, pp.11-16, 2008.
DOI : 10.1097/QAD.0b013e32830ebcd4

L. Swenson, T. Mo, W. Dong, X. Zhong, C. Woods et al., Deep Sequencing to Infer HIV-1 Co-Receptor Usage: Application to Three Clinical Trials of Maraviroc in Treatment-Experienced Patients, Journal of Infectious Diseases, vol.203, issue.2, pp.237-245, 2011.
DOI : 10.1093/infdis/jiq030

R. Kagan, E. Johnson, M. Siaw, P. Biswas, D. Chapman et al., A Genotypic Test for HIV-1 Tropism Combining Sanger Sequencing with Ultradeep Sequencing Predicts Virologic Response in Treatment-Experienced Patients, PLoS ONE, vol.7, issue.9, p.23029482, 2012.
DOI : 10.1371/journal.pone.0046334.s004

A. Saliou, P. Delobel, M. Dubois, F. Nicot, R. S. Calvez et al., Concordance between Two Phenotypic Assays and Ultradeep Pyrosequencing for Determining HIV-1 Tropism, Antimicrobial Agents and Chemotherapy, vol.55, issue.6, pp.2831-2836, 2011.
DOI : 10.1128/AAC.00091-11

URL : https://hal.archives-ouvertes.fr/hal-00675722

R. Gibson, A. Meyer, D. Winner, J. Archer, F. Feyertag et al., Sensitive Deep-Sequencing-Based HIV-1 Genotyping Assay To Simultaneously Determine Susceptibility to Protease, Reverse Transcriptase, Integrase, and Maturation Inhibitors, as Well as HIV-1 Coreceptor Tropism, Antimicrobial Agents and Chemotherapy, vol.58, issue.4, pp.2167-2185, 2014.
DOI : 10.1128/AAC.02710-13

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023761

D. Jong, J. De-ronde, A. Keulen, W. Tersmette, M. Goudsmit et al., Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: analysis by single amino acid substitution, J Virol, vol.66, pp.6777-6780, 1992.

T. Lengauer, O. Sander, S. Sierra, A. Thielen, and R. Kaiser, Bioinformatics prediction of HIV coreceptor usage, Nature Biotechnology, vol.12, issue.12, pp.1407-1410, 2007.
DOI : 10.1007/s00894-003-0154-9

M. Daumer, R. Kaiser, R. Klein, T. Lengauer, B. Thiele et al., Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis, BMC Medical Informatics and Decision Making, vol.2009, issue.1, p.21569501, 2011.
DOI : 10.1097/QAD.0b013e32833e6cfb

P. Recordon-pinson, C. Soulie, P. Flandre, D. Descamps, M. Lazrek et al., Evaluation of the Genotypic Prediction of HIV-1 Coreceptor Use versus a Phenotypic Assay and Correlation with the Virological Response to Maraviroc: the ANRS GenoTropism Study, Antimicrobial Agents and Chemotherapy, vol.54, issue.8, pp.3335-3340, 2010.
DOI : 10.1128/AAC.00148-10

URL : https://hal.archives-ouvertes.fr/hal-00594694

C. Rodriguez, S. Chevaliez, P. Bensadoun, and J. Pawlotsky, Characterization of the dynamics of hepatitis B virus resistance to adefovir by ultra-deep pyrosequencing, Hepatology, vol.54, issue.Suppl 1, pp.890-901, 2013.
DOI : 10.1002/hep.26383

URL : https://hal.archives-ouvertes.fr/inserm-00936562

L. Vandekerckhove, C. Verhofstede, E. Demecheleer, D. Wit, S. Florence et al., Comparison of phenotypic and genotypic tropism determination in triple-class-experienced HIV patients eligible for maraviroc treatment, Journal of Antimicrobial Chemotherapy, vol.66, issue.2, pp.265-272, 2011.
DOI : 10.1093/jac/dkq458

E. Poveda, R. Paredes, S. Moreno, J. Alcami, J. Cordoba et al., Update on clinical and methodological recommendations for genotypic determination of HIV tropism to guide the usage of CCR5 antagonists, AIDS Rev, vol.14, pp.208-217, 2012.

D. Altshuler, V. Pollara, C. Cowles, W. Van-etten, J. Baldwin et al., An SNP map of the human genome generated by reduced representation shotgun sequencing, Nature, vol.407, pp.513-516, 2000.

P. Delobel, M. Nugeyre, M. Cazabat, C. Pasquier, B. Marchou et al., Population-Based Sequencing of the V3 Region of env for Predicting the Coreceptor Usage of Human Immunodeficiency Virus Type 1 Quasispecies, Journal of Clinical Microbiology, vol.45, issue.5, pp.1572-1580, 2007.
DOI : 10.1128/JCM.02090-06

L. Swenson, T. Mo, W. Dong, X. Zhong, C. Woods et al., Deep V3 Sequencing for HIV Type 1 Tropism in Treatment-Naive Patients: A Reanalysis of the MERIT Trial of Maraviroc, Clinical Infectious Diseases, vol.53, issue.7, pp.732-742, 2011.
DOI : 10.1093/cid/cir493

A. Bandos, H. Rockette, and D. Gur, A permutation test sensitive to differences in areas for comparing ROC curves from a paired design, Statistics in Medicine, vol.56, issue.18, pp.2873-2893, 2005.
DOI : 10.1002/sim.2149

X. Robin, N. Turck, A. Hainard, N. Tiberti, F. Lisacek et al., pROC: an open-source package for R and S+ to analyze and compare ROC curves, BMC Bioinformatics, vol.12, issue.1, p.77, 2011.
DOI : 10.1007/s00134-009-1641-y

L. Swenson, T. Mo, W. Dong, X. Zhong, C. Woods et al., Deep Sequencing to Infer HIV-1 Co-Receptor Usage: Application to Three Clinical Trials of Maraviroc in Treatment-Experienced Patients, Journal of Infectious Diseases, vol.203, issue.2, pp.237-245, 2011.
DOI : 10.1093/infdis/jiq030

M. Chen, V. Svicher, A. Artese, G. Costa, C. Alteri et al., Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage, Bioinformatics, vol.29, issue.4, pp.451-460, 2013.
DOI : 10.1093/bioinformatics/btt002