Q. Li, X. Guan, P. Wu, X. Wang, L. Zhou et al., Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia, New England Journal of Medicine, 2020.

, Coronaviridae Study Group of the ICTV. The species Severe acute respiratory syndrome-related coronavirus : classifying 2019-nCoV and naming it SARS-CoV-2, Nat Microbiol, vol.2020, pp.1-9

H. D. Song, C. C. Tu, G. W. Zhang, S. Y. Wang, K. Zheng et al., Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human, Proceedings of the National Academy of Sciences, vol.102, issue.7, pp.2430-2435, 2005.

M. F. Boni, P. Lemey, X. Jiang, T. Lam, B. Perry et al., Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

K. G. Andersen, A. Rambaut, W. I. Lipkin, E. C. Holmes, and R. F. Garry, The proximal origin of SARS-CoV-2, Nat Med, vol.2020, pp.1-3

H. Zhou, X. Chen, T. Hu, J. Li, H. Song et al., A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein, Current Biology, vol.30, issue.11, pp.2196-2203, 2020.

A. Rambaut, Phylodynamic Analysis | 176 genomes |, vol.2020, 2020.

B. T. Grenfell, O. G. Pybus, J. R. Gog, J. L. Wood, J. M. Daly et al., Unifying the Epidemiological and Evolutionary Dynamics of Pathogens, Science, vol.303, issue.5656, pp.327-332, 2004.

E. M. Volz, K. Koelle, and T. Bedford, Viral Phylodynamics, PLoS Computational Biology, vol.9, issue.3, p.e1002947, 2013.

S. D. Frost, O. G. Pybus, J. R. Gog, C. Viboud, S. Bonhoeffer et al., Eight challenges in phylodynamic inference, Epidemics, vol.10, pp.88-92, 2015.

S. Alizon and E. Saulnier, Prévention et traitement de maladies virales par des vaccins nouveaux et par la chimiothérapie, Annales de l'Institut Pasteur / Virologie, vol.136, issue.4, p.2, 1985.

E. Volz, M. Baguelin, S. Bhatia, A. Boonyasiri, A. Cori et al., Phylogenetic analysis of SARS-CoV-2, vol.5, p.7

J. Scire, T. G. Vaughan, and T. Stadler, Phylodynamic analyses based on 93 genomes, 2020.

P. Lemey, A. Rambaut, A. J. Drummond, and M. A. Suchard, Bayesian phylogeography finds its roots, PLoS Comput Biol, vol.5, issue.9, p.1000520, 2009.

P. Sagulenko, V. Puller, and R. A. Neher, TreeTime : Maximum-likelihood phylodynamic analysis, Virus Evol, vol.4, issue.1, 2018.

J. Hadfield, C. Megill, S. M. Bell, J. Huddleston, B. Potter et al., Nextstrain : real-time tracking of pathogen evolution, Bioinformatics, vol.34, issue.23, pp.4121-4123, 2018.

S. M. Bell, E. Hodcroft, N. Müller, C. Wagner, J. Hadfield et al., Genomic analysis of nCoV spread, 2020.

A. Rambaut, E. C. Holmes, V. Hill, A. O'toole, J. T. Mccrone et al., A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

X. Deng, W. Gu, S. Federman, P. Ld, O. G. Pybus et al., Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California, Science, 2020.

G. Danesh, B. Elie, Y. Michalakis, M. T. Sofonea, A. Bal et al., Early phylodynamics analysis of the COVID-19 epidemics in France, 20119925.

M. T. Sofonea, B. Reyné, B. Elie, R. Djidjou-demasse, C. Selinger et al., Epidemiological monitoring and control perspectives : application of a parsimonious modelling framework to the COVID-19 dynamics in France, 20110593.
URL : https://hal.archives-ouvertes.fr/hal-02619546

R. M. Anderson and R. M. May, Infectious Diseases of Humans, Dynamics and Control, 1991.

H. Salje, C. T. Kiem, N. Lefrancq, N. Courtejoie, P. Bosetti et al., Estimating the burden of SARS-CoV-2 in France, HAL, vol.2020, p.2548181
URL : https://hal.archives-ouvertes.fr/pasteur-02548181

T. Stadler, D. Kühnert, S. Bonhoeffer, and A. J. Drummond, Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV), Proc Natl Acad Sci, vol.110, issue.1, pp.228-261, 2013.

L. Ferretti, C. Wymant, M. Kendall, L. Zhao, A. Nurtay et al., Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing, Science, 2020.

S. K. Gire, A. Goba, K. G. Andersen, R. Sealfon, D. J. Park et al., Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak, Science, vol.345, issue.6202, pp.1369-72, 2014.

J. Quick, N. J. Loman, S. Duraffour, J. T. Simpson, E. Severi et al., Real-time, portable genome sequencing for Ebola surveillance, Nature, vol.530, issue.7589, pp.228-232, 2016.

M. Hartfield, C. L. Murall, and S. Alizon, Clinical applications of pathogen phylogenies, Trends Mol Med, vol.20, issue.7, pp.394-404, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01567914

Z. Shen, Y. Xiao, L. Kang, W. Ma, L. Shi et al., Genomic Diversity of Severe Acute Respiratory Syndrome-Coronavirus 2 in Patients With Coronavirus Disease, Clin Infect Dis, 2019.

K. A. Lythgoe, M. D. Hall, L. Ferretti, C. Md, G. Macintyre-cockett et al., Shared SARS-CoV-2 diversity suggests localised transmission of minority variants

I. Schuffenecker, I. Iteman, A. Michault, S. Murri, L. Frangeul et al., Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak, PLoS Med, vol.3, issue.7, p.263, 2006.
URL : https://hal.archives-ouvertes.fr/pasteur-01659363

R. A. Urbanowicz, C. P. Mcclure, A. Sakuntabhai, A. A. Sall, G. Kobinger et al., Human Adaptation of Ebola Virus during the West African Outbreak, Cell, vol.167, issue.4, pp.1079-1087, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-02003921

S. Alizon and P. O. Méthot, Reconciling Pasteur and Darwin to control infectious diseases, PLoS Biol, vol.16, issue.1, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01737461

, Date

F. ,

F. ,

/. France and . Cibu-, , 2020.

F. , , 2020.

F. ,

F. ,

/. France and . Occ,

F. , France, 2020.

F. ,

F. ,

F. ,

, Cet arbre a été téléchargé le 4 juillet 2020 [15, 16] et obtenu à parir des données de la base GISAID. Les couleurs indiquent les continents sur lesquels ont eu lieu les infections. 57 feuilles correspondant à des séquences issues d'infections en France sont indiquées par des points jaunes. La majorité des séquences, qui appartiennent a priori à la vague épidémique, FIGURE 1 -Phylogénie d'infections de la pandémie de COVID-19 obtenu par Nextstrain