M. Anisimova and O. Gascuel, Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative, Syst. Biol, vol.55, pp.539-552, 2006.
URL : https://hal.archives-ouvertes.fr/lirmm-00136658

T. Azarian, A. Lo-presti, M. Giovanetti, E. Cella, B. Rife et al., Impact of spatial dispersion, evolution, and selection on Ebola Zaire Virus epidemic waves, Sci. Rep, vol.5, p.10170, 2015.

C. Besnier, L. Ylinen, B. Strange, A. Lister, Y. Takeuchi et al., Characterization of murine leukemia virus restriction in mammals, J. Virol, vol.77, pp.13403-13406, 2003.

M. R. Capobianchi, C. E. Gruber, F. Carletti, S. Meschi, C. Castilletti et al., Molecular signature of the ebola virus associated with the fishermen community outbreak in, Genome Announc. Published on, 2015.

M. W. Carroll, D. A. Matthews, J. A. Hiscox, M. J. Elmore, G. Pollakis et al., Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa, Nature, vol.524, pp.97-101, 2015.

W. E. Diehl, A. E. Lin, N. D. Grubaugh, L. M. Carvalho, K. Kyusik et al., Ebola virus glycoprotein with increased infectivity dominated the 2013-2016 epidemic, vol.167, pp.1088-1098, 2016.

O. Faye, A. Andronico, O. Faye, H. Salje, P. Y. Boë-lle et al., Use of Viremia to Evaluate the Baseline Case Fatality Ratio of Ebola Virus Disease and Inform Treatment Studies: A Retrospective Cohort Study, PLoS Med, vol.12, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01274833

G. Fitzpatrick, F. Vogt, O. B. Moi-gbabai, T. Decroo, M. Keane et al., The Contribution of Ebola Viral Load at Admission and Other Patient Characteristics to Mortality in a Medecins Sans Frontieres Ebola Case Management Centre, J. Infect. Dis, vol.212, pp.1752-1758, 2014.

S. K. Gire, A. Goba, K. G. Andersen, R. S. Sealfon, D. J. Park et al., Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak, Science, vol.345, pp.1369-1372, 2014.

X. Gong, H. Qian, X. Zhou, J. Wu, T. Wan et al., Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection, Cell, vol.165, pp.1467-1478, 2016.

S. Guindon, J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

B. A. Han, J. P. Schmidt, L. W. Alexander, S. E. Bowden, D. T. Hayman et al., Undiscovered Bat Hosts of Filoviruses, PLoS Negl. Trop. Dis, vol.10, p.4815, 2016.

C. Herrera, P. J. Klasse, E. Michael, S. Kake, K. Barnes et al., The impact of envelope glycoprotein cleavage on the antigenicity, infectivity, and neutralization sensitivity of Env-pseudotyped human immunodeficiency virus type 1 particles, Virology, vol.338, pp.154-172, 2005.

T. Hoenen, D. Safronetz, A. Groseth, K. R. Wollenberg, O. A. Koita et al., Virology. Mutation rate and genotype variation of Ebola virus from Mali case sequences, Science, vol.348, pp.117-119, 2015.

A. Kuhl, M. Hoffmann, M. A. Muller, V. J. Munster, K. Gnirss et al., Comparative analysis of Ebola virus glycoprotein interactions with human and bat cells, J. Infect. Dis, vol.204, issue.3, pp.840-849, 2011.

J. T. Ladner, M. R. Wiley, S. Mate, G. Dudas, K. Prieto et al., Evolution and Spread of Ebola Virus in Liberia, Cell Host Microbe, vol.18, pp.659-669, 2014.

J. E. Lee, M. L. Fusco, A. J. Hessell, W. B. Oswald, D. R. Burton et al., Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor, Nature, vol.454, pp.177-182, 2008.

S. A. Leendertz, J. F. Gogarten, A. Dü-x, S. Calvignac-spencer, and F. H. Leendertz, Assessing the Evidence Supporting Fruit Bats as the Primary Reservoirs for Ebola Viruses, EcoHealth, vol.13, pp.18-25, 2016.

N. J. Lennemann, B. A. Rhein, E. Ndungo, K. Chandran, X. Qiu et al., Comprehensive functional analysis of N-linked glycans on Ebola virus GP1, MBio, vol.5, pp.862-875, 2014.

E. M. Leroy, B. Kumulungui, X. Pourrut, P. Rouquet, A. Hassanin et al., Fruit bats as reservoirs of Ebola virus, Nature, vol.438, pp.575-576, 2005.

S. Q. Liu, C. L. Deng, Z. M. Yuan, S. Rayner, and B. Zhang, Identifying the pattern of molecular evolution for Zaire ebolavirus in the 2014 outbreak in West Africa, Infect. Genet. Evol, vol.32, pp.51-59, 2015.

A. Marí-saé-z, S. Weiss, K. Nowak, V. Lapeyre, F. Zimmermann et al., Investigating the zoonotic origin of the West African Ebola epidemic, EMBO Mol. Med, vol.7, pp.17-23, 2014.

O. Martinez, E. Ndungo, L. Tantral, E. H. Miller, L. W. Leung et al., A mutation in the Ebola virus envelope glycoprotein restricts viral entry in a host species-and cell-type-specific manner, J. Virol, vol.87, pp.3324-3334, 2013.

A. Marzi, A. Akhavan, G. Simmons, T. Gramberg, H. Hofmann et al., The signal peptide of the ebolavirus glycoprotein influences interaction with the cellular lectins DC-SIGN and DCSIGNR, J. Virol, vol.80, pp.6305-6317, 2006.

G. S. Mohan, L. Ye, W. Li, A. Monteiro, X. Lin et al., Less is more: Ebola virus surface glycoprotein expression levels regulate virus production and infectivity, J. Virol, vol.89, pp.1205-1217, 2015.

L. H. Moncla, G. Zhong, C. W. Nelson, J. M. Dinis, J. Mutschler et al., Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus, Cell Host Microbe, vol.19, pp.169-180, 2016.

H. Nakabayashi, K. Taketa, K. Miyano, T. Yamane, and J. Sato, , 1982.

, Growth of human hepatoma cells lines with differentiated functions in chemically defined medium, Cancer Res, vol.42, pp.3858-3863

M. Ng, E. Ndungo, M. E. Kaczmarek, A. S. Herbert, T. Binger et al., Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats, vol.4, p.11785, 2015.

H. Ogawa, H. Miyamoto, E. Nakayama, R. Yoshida, I. Nakamura et al., Seroepidemiological Prevalence of Multiple Species of Filoviruses in Fruit Bats (Eidolon helvum) Migrating in Africa, J. Infect. Dis, vol.212, issue.2, pp.101-108, 2015.

A. S. Olabode, X. Jiang, D. L. Robertson, L. , and S. C. , Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak, Virology, vol.482, pp.202-207, 2015.

D. Olal, A. I. Kuehne, S. Bale, P. Halfmann, T. Hashiguchi et al., Structure of an antibody in complex with its mucin domain linear epitope that is protective against Ebola virus, J. Virol, vol.86, pp.2809-2816, 2012.

K. M. Pepin, S. Lass, J. R. Pulliam, A. F. Read, L. et al., Identifying genetic markers of adaptation for surveillance of viral host jumps, Nat. Rev. Microbiol, vol.8, pp.802-813, 2010.

X. Pourrut, A. Dé-licat, P. E. Rollin, T. G. Ksiazek, J. P. Gonzalez et al., Spatial and temporal patterns of Zaire ebolavirus antibody prevalence in the possible reservoir bat species, J. Infect. Dis, vol.196, issue.2, pp.176-183, 2007.

X. Pourrut, M. Souris, J. S. Towner, P. E. Rollin, S. T. Nichol et al., Large serological survey showing cocirculation of Ebola and Marburg viruses in Gabonese bat populations, and a high seroprevalence of both viruses in Rousettus aegyptiacus, BMC Infect. Dis, vol.9, p.159, 2009.

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, pp.228-232, 2016.

R. R. Reddel, K. Yang, J. S. Rhim, D. Brash, R. T. Su et al., Immortalized human bronchial epithelial mesothelial cell lines, 1989.

J. S. Schieffelin, J. G. Shaffer, A. Goba, M. Gbakie, S. K. Gire et al., KGH Lassa Fever Program; Viral Hemorrhagic Fever Consortium; WHO Clinical Response Team, N. Engl. J. Med, vol.371, pp.2092-2100, 2014.

E. Simon-loriere, O. Faye, O. Faye, L. Koivogui, N. Magassouba et al., Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic, Nature, vol.524, pp.102-104, 2015.

B. T. Smith, Cell line A549: a model system for the study of alveolar type II cell function, Am. Rev. Respir. Dis, vol.115, pp.285-293, 1977.

R. Swanepoel, P. A. Leman, F. J. Burt, N. A. Zachariades, L. E. Braack et al., Experimental inoculation of plants and animals with Ebola virus, Emerg. Infect. Dis, vol.2, pp.321-325, 1996.

Y. G. Tong, W. F. Shi, L. Di, J. Qian, L. Liang et al., Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone, Nature, vol.524, pp.93-96, 2015.

R. A. Urbanowicz, C. P. Mcclure, B. King, C. P. Mason, J. K. Ball et al., Novel functional hepatitis C virus glycoprotein isolates identified using an optimized viral pseudotype entry assay, J. Gen. Virol, vol.97, pp.2265-2279, 2016.

H. Wang, Y. Shi, J. Song, J. Qi, G. Lu et al., Ebola Viral Glycoprotein Bound to Its Endosomal Receptor Niemann-Pick C1, Cell, vol.164, pp.258-268, 2016.

W. H. , Ebola Situation Report, 2016.

M. W. Yap, E. Colbeck, S. A. Ellis, and J. P. Stoye, Evolution of the retroviral restriction gene Fv1: inhibition of non-MLV retroviruses, PLoS Pathog, vol.10, pp.1079-1087, 2014.