C. Fraser, C. Donnelly, S. Cauchemez, W. Hanage, and M. Van-kerkhove, Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings, Science, vol.360, issue.25, pp.1557-1561, 2009.
DOI : 10.1056/NEJMoa0903810

F. Dawood, S. Jain, L. Finelli, M. Shaw, and S. Lindstrom, Emergence of a novel swine-origin influenza A (H1N1) virus in humans, N Engl J Med, vol.360, pp.2605-2615, 2009.

R. Garten, C. Davis, C. Russell, B. Shu, and S. Lindstrom, Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans, Science, vol.14, issue.9, pp.197-201, 2009.
DOI : 10.1093/bioinformatics/14.9.817

URL : http://science.sciencemag.org/content/sci/325/5937/197.full.pdf

D. Balcan, H. Hu, B. Goncalves, P. Bajardi, and C. Poletto, Seasonal transmission potential and activity peaks of the new influenza A(H1N1): a Monte Carlo likelihood analysis based on human mobility, BMC Medicine, vol.116, issue.1, p.45, 2009.
DOI : 10.1289/ehp.11310

URL : https://hal.archives-ouvertes.fr/hal-00421835

M. Nelson, D. Spiro, D. Wentworth, E. Beck, and J. Fan, The early diversification of influenza A/H1N1pdm, PLoS Currents, vol.1, p.1126, 2009.
DOI : 10.1371/currents.RRN1126

URL : http://currents.plos.org/influenza/article/the-early-diversification-of-influenza-ah1n1pdm/pdf/

V. Potdar, M. Chadha, S. Jadhav, J. Mullick, and S. Cherian, Genetic Characterization of the Influenza A Pandemic (H1N1) 2009 Virus Isolates from India, PLoS ONE, vol.5, issue.3, p.9693, 2010.
DOI : 10.1371/journal.pone.0009693.t003

T. Ilyicheva, I. Susloparov, A. Durymanov, A. Romanovskaya, and K. Sharshov, Influenza A/H1N1pdm virus in Russian Asia, Infect Genet Evol, 2009.
DOI : 10.1016/j.meegid.2011.05.002

P. Barrero, M. Viegas, L. Valinotto, and A. Mistchenko, Genetic and Phylogenetic Analyses of Influenza A H1N1pdm Virus in Buenos Aires, Argentina, Journal of Virology, vol.85, issue.2, pp.1058-1066, 2011.
DOI : 10.1128/JVI.00936-10

K. Chan, K. To, I. Hung, A. Zhang, and J. Chan, ABSTRACT, Clinical and Vaccine Immunology, vol.18, issue.5, pp.867-873, 2011.
DOI : 10.1128/CVI.00555-10

URL : https://hal.archives-ouvertes.fr/hal-01377942

Y. Furuse, A. Suzuki, and H. Oshitani, Evolutionary analyses on the HA gene of pandemic H1N1/09: early findings, Bioinformation, vol.5, issue.1, pp.7-10, 2010.
DOI : 10.6026/97320630005007

T. Shiino, N. Okabe, Y. Yasui, T. Sunagawa, and M. Ujike, Molecular Evolutionary Analysis of the Influenza A(H1N1)pdm, May???September, 2009: Temporal and Spatial Spreading Profile of the Viruses in Japan, PLoS ONE, vol.20, issue.6, p.11057, 2009.
DOI : 10.1371/journal.pone.0011057.s006

D. Parks, N. Macdonald, and R. Beiko, Tracking the evolution and geographic spread of Influenza A, PLoS currents, vol.1, p.1014, 2009.

E. Pariani, A. Piralla, E. Frati, G. Anselmi, and G. Campanini, Early cocirculation of different clades of influenza A/H1N1v pandemic virus in northern Italy, Journal of preventive medicine and hygiene, vol.52, pp.17-20, 2011.

M. Graham, B. Liang, G. Van-domselaar, N. Bastien, and C. Beaudoin, Nationwide Molecular Surveillance of Pandemic H1N1 Influenza A Virus Genomes: Canada, 2009, PLoS ONE, vol.22, issue.5, p.16087, 2009.
DOI : 10.1371/journal.pone.0016087.s011

D. Balcan, H. Hu, B. Goncalves, P. Bajardi, and C. Poletto, Seasonal transmission potential and activity peaks of the new influenza A(H1N1): a Monte Carlo likelihood analysis based on human mobility, BMC Medicine, vol.116, issue.1, p.45, 2009.
DOI : 10.1289/ehp.11310

URL : https://hal.archives-ouvertes.fr/hal-00421835

J. Brownstein, C. Wolfe, and K. Mandl, Empirical Evidence for the Effect of Airline Travel on Inter-Regional Influenza Spread in the United States, PLoS Medicine, vol.286, issue.10, p.401, 2006.
DOI : 10.1371/journal.pmed.0030401.sd001

D. Ortenzio, E. , R. P. Jaffar-bandjee, M. Gauzere, B. Lagrange-xelot et al., A review of the dynamics and severity of the pandemic A(H1N1) influenza virus on R??union Island, 2009, Clinical Microbiology and Infection, vol.16, issue.4, pp.309-316, 2009.
DOI : 10.1111/j.1469-0691.2010.03171.x

K. Dellagi, O. Rollot, S. Temmam, N. Salez, and V. Guernier, Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009, PLoS ONE, vol.6, issue.2, p.25738, 2009.
DOI : 10.1371/journal.pone.0025738.t004

URL : https://hal.archives-ouvertes.fr/halsde-00724649

O. Koita, L. Sangare, B. Poudiougou, B. Aboubacar, and Y. Samake, A seroepidemiological study of pandemic A/H1N1(2009) influenza in a rural population of Mali. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 2011.

L. Ninove, A. Nougairede, C. Gazin, L. Thirion, and I. Delogu, RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests, PLoS ONE, vol.45, issue.2, p.16142, 2011.
DOI : 10.1371/journal.pone.0016142.s004

L. Ninove, C. Gazin, E. Gould, A. Nougairede, and A. Flahault, A Simple Method for Molecular Detection of Swine-Origin and Human-Origin Influenza A Virus, Vector-Borne and Zoonotic Diseases, vol.10, issue.3, pp.237-240, 2009.
DOI : 10.1089/vbz.2009.0110

O. Zhirnov, I. Vorobjeva, O. Saphonova, S. Poyarkov, and A. Ovcharenko, Structural and evolutionary characteristics of HA, NA, NS and M genes of clinical influenza A/H3N2 viruses passaged in human and canine cells, Journal of Clinical Virology, vol.45, issue.4, pp.322-333, 2009.
DOI : 10.1016/j.jcv.2009.05.030

A. Drummond, B. Ashton, S. Buxton, M. Cheung, and A. Cooper, , 2010.

R. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, p.113, 2004.
DOI : 10.1186/1471-2105-5-113

D. Posada, jModelTest: Phylogenetic Model Averaging, Molecular Biology and Evolution, vol.39, issue.3, pp.1253-1256, 2008.
DOI : 10.1007/BF00160155

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

F. Ronquist and J. Huelsenbeck, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, vol.19, issue.12, pp.1572-1574, 2003.
DOI : 10.1093/bioinformatics/btg180

K. Tamura, D. Peterson, N. Peterson, G. Stecher, and M. Nei, MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.141, issue.3, pp.2731-2739, 2011.
DOI : 10.1007/BF00160154

F. Tajima and M. Nei, Estimation of evolutionary distance between nucleotide sequences, Molecular biology and evolution, vol.1, pp.269-285, 1984.

A. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, p.214, 2007.
DOI : 10.1186/1471-2148-7-214

N. Goni, A. Fajardo, G. Moratorio, R. Colina, and C. J. , Modeling gene sequences over time in 2009 H1N1 Influenza A Virus populations, Virology Journal, vol.6, issue.1, p.215, 2009.
DOI : 10.1186/1743-422X-6-215

M. Nelson and E. Holmes, The evolution of epidemic influenza, Nature Reviews Genetics, vol.36, issue.3, pp.196-205, 2007.
DOI : 10.3201/eid1001.020705

M. Nelson, D. Spiro, D. Wentworth, E. Beck, and J. Fan, The early diversification of influenza A/H1N1pdm, PLoS Currents, vol.1, p.1126, 2009.
DOI : 10.1371/currents.RRN1126

Y. Furuse, A. Suzuki, and H. Oshitani, Reassortment between swine influenza A viruses increased their adaptation to humans in pandemic H1N1/09. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, pp.569-574, 2010.

O. Ferraris and L. B. , Mutations of neuraminidase implicated in neuraminidase inhibitors resistance, Journal of Clinical Virology, vol.41, issue.1, pp.13-19, 2008.
DOI : 10.1016/j.jcv.2007.10.020

M. Giria, R. De-andrade, H. Santos, L. Correia, V. Pedro et al., Genomic signatures and antiviral drug susceptibility profile of A(H1N1)pdm09, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2011.
DOI : 10.1016/j.jcv.2011.11.002

G. Glinsky, Genomic analysis of pandemic (H1N1) 2009 reveals association of increasing disease severity with emergence of novel hemagglutinin mutations, Cell Cycle, vol.9, issue.5, pp.958-970, 2010.
DOI : 10.4161/cc.9.5.10913

A. Reid, T. Fanning, J. Hultin, and J. Taubenberger, Origin and evolution of the 1918 "Spanish" influenza virus hemagglutinin gene, Proceedings of the National Academy of Sciences, vol.66, issue.2, pp.1651-1656, 1999.
DOI : 10.1084/jem.63.5.669

H. Tse, R. Kao, W. Wu, W. Lim, and H. Chen, Structural basis and sequence co-evolution analysis of the hemagglutinin protein of pandemic influenza A/H1N1 (2009) virus, Experimental Biology and Medicine, vol.267, issue.8, pp.915-925, 2011.
DOI : 10.1073/pnas.0807142105

H. Chen, X. Wen, K. To, P. Wang, and H. Tse, Quasispecies of the D225G Substitution in the Hemagglutinin of Pandemic Influenza A(H1N1) 2009 Virus from Patients with Severe Disease in Hong Kong, China, The Journal of Infectious Diseases, vol.201, issue.10, pp.1517-1521, 2010.
DOI : 10.1086/652661

H. Tse, K. To, X. Wen, H. Chen, and K. Chan, Clinical and Virological Factors Associated with Viremia in Pandemic Influenza A/H1N1/2009 Virus Infection, PLoS ONE, vol.7, issue.9, p.22534, 2011.
DOI : 10.1371/journal.pone.0022534.t002

A. Zhang, K. To, H. Tse, K. Chan, and K. Guo, ABSTRACT, Clinical and Vaccine Immunology, vol.18, issue.11, pp.1918-1924, 2011.
DOI : 10.1128/CVI.05357-11

URL : https://hal.archives-ouvertes.fr/hal-01215041

L. Filleul, D. Ortenzio, E. Kermarec, F. , L. Bot et al., Pandemic influenza on Reunion Island and school closure, The Lancet Infectious Diseases, vol.10, issue.5, pp.294-295, 2010.
DOI : 10.1016/S1473-3099(10)70076-1

H. Kelly, G. Mercer, J. Fielding, G. Dowse, and K. Glass, Pandemic (H1N1) 2009 Influenza Community Transmission Was Established in One Australian State When the Virus Was First Identified in North America, PLoS ONE, vol.15, issue.6, p.11341, 2010.
DOI : 10.1371/journal.pone.0011341.t001

D. Chao, K. Cheng, T. Li, T. Wu, and C. Chen, Serological Evidence of Subclinical Transmission of the 2009 Pandemic H1N1 Influenza Virus Outside of Mexico, PLoS ONE, vol.361, issue.27, p.14555, 2011.
DOI : 10.1371/journal.pone.0014555.t002

L. Gubareva, D. Novikov, and F. Hayden, Assessment of Hemagglutinin Sequence Heterogeneity during Influenza Virus Transmission in Families, The Journal of Infectious Diseases, vol.186, issue.11, pp.1575-1581, 2002.
DOI : 10.1086/345372

L. Poon, K. Chan, D. Chu, C. Fung, and C. Cheng, Viral genetic sequence variations in pandemic H1N1/2009 and seasonal H3N2 influenza viruses within an individual, a household and a community, Journal of Clinical Virology, vol.52, issue.2, pp.146-150, 2011.
DOI : 10.1016/j.jcv.2011.06.022

URL : https://hal.archives-ouvertes.fr/pasteur-00614344

P. Boelle, S. Ansart, C. A. Valleron, and A. , Transmission parameters of the A/H1N1 (2009) influenza virus pandemic: a review, Influenza and Other Respiratory Viruses, vol.5, issue.5, pp.306-316, 2011.
DOI : 10.1371/journal.pone.0011341

M. Nelson and E. Holmes, The evolution of epidemic influenza, Nature Reviews Genetics, vol.36, issue.3, pp.196-205, 2007.
DOI : 10.3201/eid1001.020705

E. Ghedin, J. Laplante, J. Depasse, D. Wentworth, and R. Santos, Deep Sequencing Reveals Mixed Infection with 2009 Pandemic Influenza A (H1N1) Virus Strains and the Emergence of Oseltamivir Resistance, The Journal of Infectious Diseases, vol.53, issue.2, pp.168-174, 2011.
DOI : 10.1128/AAC.00334-09

A. Greninger, E. Chen, T. Sittler, A. Scheinerman, and N. Roubinian, A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America, PLoS ONE, vol.2, issue.10, p.13381, 2010.
DOI : 10.1371/journal.pone.0013381.s005

A. Lauring and R. Andino, Quasispecies Theory and the Behavior of RNA Viruses, PLoS Pathogens, vol.7, issue.7, p.1001005, 2010.
DOI : 10.1371/journal.ppat.1001005.g004