A. U. Scherrer, V. Von-wyl, and W. L. Yang,

C. Swiss and . Study, Emergence of acquired HIV-1 drug resistance almost stopped in Switzerland: a 15-year prospective cohort analysis, Clin Infect Dis, vol.62, pp.1310-1317, 2016.

R. J. Smith, J. T. Okano, J. S. Kahn, E. N. Bodine, and S. Blower, Evolutionary dynamics of complex networks of HIV drug-resistant strains: the case of San Francisco, Science, vol.327, pp.697-701, 2010.

V. Jain, T. Liegler, and E. Vittinghoff, Transmitted drug resistance in persons with acute/early HIV-1 in San Francisco, PLoS One, vol.5, p.15510, 2002.

C. J. Villabona-arenas, N. Vidal, and E. Guichet, In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa, AIDS, vol.30, pp.2577-89, 2016.
URL : https://hal.archives-ouvertes.fr/lirmm-01396974

V. Cambiano, S. Bertagnolio, and M. R. Jordan, Predicted levels of HIV drug resistance: potential impact of expanding diagnosis, retention, and eligibility criteria for antiretroviral therapy initiation, AIDS, vol.28, issue.1, pp.15-23, 2014.

S. Mccormack, D. T. Dunn, and M. Desai, Pre-exposure prophylaxis to prevent the acquisition of HIV-1 infection (PROUD): effectiveness results from the pilot phase of a pragmatic open-label randomised trial, Lancet, vol.387, pp.53-60, 2016.

J. M. Molina, C. Capitant, and B. Spire, On-demand preexposure prophylaxis in men at high risk for HIV-1 infection, ANRS IPERGAY Study Group, vol.373, pp.2237-2283, 2015.
URL : https://hal.archives-ouvertes.fr/halshs-01429281

D. C. Knox, P. L. Anderson, P. R. Harrigan, and D. H. Tan, Multidrug-resistant HIV-1 infection despite preexposure prophylaxis, N Engl J Med, vol.376, pp.501-503, 2017.

U. L. Abbas, R. Glaubius, A. Mubayi, G. Hood, and J. W. Mellors, Antiretroviral therapy and pre-exposure prophylaxis: combined impact on HIV transmission and drug resistance in south africa, J Infect Dis, vol.208, pp.224-258, 2013.

V. Supervie, J. G. Garcia-lerma, W. Heneine, S. Blower, and . Hiv, Proc Natl Acad Sci U S A, vol.107, pp.12381-12387, 2010.

V. Supervie, M. Barrett, and J. S. Kahn, Modeling dynamic interactions between pre-exposure prophylaxis interventions & treatment programs: predicting HIV transmission & resistance, Sci Rep, vol.1, p.185, 2011.

M. Fisher, D. Pao, and A. E. Brown, Determinants of HIV-1 transmission in men who have sex with men: a combined clinical, epidemiological and phylogenetic approach, AIDS, vol.24, pp.1739-1786, 2010.

B. G. Brenner, M. Roger, and J. P. Routy, Quebec Primary HIV Infection Study Group. High rates of forward transmission events after acute/early HIV-1 infection, J Infect Dis, vol.195, pp.951-960, 2007.

O. Ratmann, A. Van-sighem, and D. Bezemer, ATHENA observational cohort. Sources of HIV infection among men having sex with men and implications for prevention, Sci Transl Med, vol.8, pp.320-322, 2016.

T. Leitner, D. Escanilla, C. Franzén, M. Uhlén, and J. Albert, Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis, Proc Natl Acad Sci, vol.93, pp.10864-10873, 1996.

J. Felsenstein, Confidence limits on phylogenies: an approach using the bootstrap, Evolution, vol.39, pp.783-91, 1985.

A. Poon, Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks, Virus Evol, vol.2, p.31, 2016.

F. Chevenet, M. Jung, M. Peeters, T. De-oliveira, and O. Gascuel, Searching for virus phylotypes, Bioinformatics, vol.29, pp.561-70, 2013.
URL : https://hal.archives-ouvertes.fr/ird-00831601

B. T. Grenfell, O. G. Pybus, and J. R. Gog, Unifying the epidemiological and evolutionary dynamics of pathogens, Science, vol.303, pp.327-359, 2004.

E. M. Volz, K. Koelle, and T. Bedford, Viral phylodynamics, PLoS Comput Biol, vol.9, p.1002947, 2013.

A. M. Wensing, D. A. Van-de-vijver, and G. Angarano, SPREAD Programme. Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management, J Infect Dis, vol.192, pp.958-66, 2005.

S. Yerly, T. Junier, and A. Gayet-ageron,

C. Swiss and . Study, The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection, AIDS, vol.23, pp.1415-1438, 2009.

A. M. Audelin, N. Lohse, N. Obel, J. Gerstoft, and L. B. Jørgensen, The incidence rate of HIV type-1 drug resistance in patients on antiretroviral therapy: a nationwide population-based Danish cohort study, Antivir Ther, vol.14, pp.995-1000, 1999.

F. Lewis, G. J. Hughes, A. Rambaut, A. Pozniak, L. Brown et al., Episodic sexual transmission of HIV revealed by molecular phylodynamics, PLoS Med, vol.5, p.50, 2008.

S. Hué, R. J. Gifford, D. Dunn, E. Fernhill, and D. Pillay,

, UK Collaborative Group on HIV Drug Resistance. Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naïve individuals, J Virol, vol.83, pp.2645-54, 2009.

R. Mourad, F. Chevennet, and D. T. Dunn,

, Anti-HIV Drug Resistance Network. A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK, UK HIV Drug Resistance Database & the Collaborative HIV, vol.29, pp.1917-1942, 2015.

W. M. Fitch, Toward defining the course of evolution: Minimum change for a specific tree topology, Syst Biol, vol.20, pp.406-422, 1971.

S. M. Drescher, V. Von-wyl, and W. L. Yang,

C. Swiss and . Study, Treatment-naive individuals are the major source of transmitted HIV-1 drug resistance in men who have sex with men in the Swiss HIV Cohort Study, Clin Infect Dis, vol.58, pp.285-94, 2014.

D. Pillay, J. Herbeck, and M. S. Cohen, PANGEA-HIV: phylogenetics for generalised epidemics in Africa, Lancet Infect Dis, vol.15, pp.259-61, 2015.

G. Yebra, E. B. Hodcroft, M. L. Ragonnet-cronin, D. Pillay, A. J. Brown et al., Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic, Sci Rep, vol.6, p.39489, 2016.