E. Strauss and J. Strauss, Structure and Replication of the Alphavirus Genome, The Togaviridae and Flaviviridae, pp.35-90, 1986.
DOI : 10.1007/978-1-4757-0785-4_3

J. Porterfield, Antigenic Characteristics and Classification of Togaviridae, The Togaviruses, pp.13-46, 1980.
DOI : 10.1016/B978-0-12-625380-1.50007-2

R. Ross, The Newala epidemic: III. The virus: isolation, pathogenic properties and relationship to the epidemic, Journal of Hygiene, vol.1, issue.02, pp.177-191, 1956.
DOI : 10.1016/0035-9203(55)90080-8

P. Jupp and B. Mcintosh, Chikungunya disease The Arboviruses: Epidemiology and ecology, Boca Raton, pp.137-157, 1988.

R. Johnston and C. Peters, Alphaviruses associated primarily with fever and polyarthritis, Fields virology. Philadelphia: Lippincott-Raven Publishers, pp.843-898, 1996.

B. Pastorino, J. Muyembe-tamfum, M. Bessaud, F. Tock, and H. Tolou, Epidemic resurgence of Chikungunya virus in democratic Republic of the Congo: Identification of a new central African strain, Journal of Medical Virology, vol.47, issue.2, pp.277-282, 2004.
DOI : 10.1099/0022-1317-81-2-471

K. Laras, N. Sukri, R. Larasati, M. Bangs, and R. Kosim, Tracking the re-emergence of epidemic chikungunya virus in Indonesia, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.99, issue.2, pp.128-141, 2005.
DOI : 10.1016/j.trstmh.2004.03.013

C. Paquet, I. Quatresous, J. Solet, D. Sissoko, and P. Renault, Chikungunya outbreak in Reunion: Epidemiology and surveillance, Euro Surveill, vol.11, issue.2, 2005.
DOI : 10.2807/esw.11.05.02891-en

A. Khan, K. Morita, P. M. Mdel, C. Hasebe, F. Mathenge et al., Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site, Journal of General Virology, vol.83, issue.12, pp.3075-3084, 2002.
DOI : 10.1099/0022-1317-83-12-3075

A. Powers, A. Brault, R. Tesh, and S. Weaver, Re-emergence of chikungunya and o???nyong-nyong viruses: evidence for distinct geographical lineages and distant evolutionary relationships, Journal of General Virology, vol.81, issue.2, pp.471-479, 2000.
DOI : 10.1099/0022-1317-81-2-471

E. Navarro-sanchez, M. Altmeyer, A. A. Schwartz, O. Fieschi, and F. , DC-SIGN is essential for the productive infection of human dendritic cells by mosquito-cell-derived dengue viruses, EMBO Rep, vol.7, pp.1-6, 2003.

D. Gordon, C. Abajian, and P. Green, A Graphical Tool for Sequence???Finishing, Genome Research, vol.70, issue.3, pp.195-202, 1998.
DOI : 10.1016/0022-2836(81)90087-5
URL : http://genome.cshlp.org/content/8/3/195.full.pdf

J. Rozas, J. Sanchez-delbarrio, X. Messeguer, and R. Rozas, DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, vol.19, issue.18, pp.2496-2497, 2003.
DOI : 10.1093/bioinformatics/btg359
URL : https://academic.oup.com/bioinformatics/article-pdf/19/18/2496/486315/btg359.pdf

X. Xia and Z. Xie, DAMBE: Software Package for Data Analysis in Molecular Biology and Evolution, Journal of Heredity, vol.92, issue.4, pp.371-373, 2001.
DOI : 10.1093/jhered/92.4.371

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

J. Felsenstein, PHYLIP?Phylogeny Inference Package (version 3.2), Cladistics, vol.5, pp.164-166, 1989.

I. Hofacker, Vienna RNA secondary structure server, Nucleic Acids Research, vol.31, issue.13, pp.3429-3431, 2003.
DOI : 10.1093/nar/gkg599

S. Kumar, K. Tamura, and M. Nei, MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment, Briefings in Bioinformatics, vol.5, issue.2, pp.150-163, 2004.
DOI : 10.1093/bib/5.2.150
URL : https://academic.oup.com/bib/article-pdf/5/2/150/9731818/150.pdf

D. Martin, C. Williamson, and D. Posada, RDP2: recombination detection and analysis from sequence alignments, Bioinformatics, vol.21, issue.2, pp.260-262, 2005.
DOI : 10.1093/bioinformatics/bth490
URL : https://academic.oup.com/bioinformatics/article-pdf/21/2/260/458930/bth490.pdf

A. Roussel, J. Lescar, M. Vaney, G. Wengler, and G. Wengler, Structure and Interactions at the Viral Surface of the Envelope Protein E1 of Semliki Forest Virus, Structure, vol.14, issue.1, pp.75-86, 2006.
DOI : 10.1016/j.str.2005.09.014

M. Carson, Ribbon models of macromolecules, Journal of Molecular Graphics, vol.5, issue.2, pp.103-106, 1987.
DOI : 10.1016/0263-7855(87)80010-3

J. Strauss and E. Strauss, The alphaviruses: Gene expression, replication, and evolution, Microbiol Rev, vol.58, pp.491-562, 1994.

A. Lavergne, B. Thoisy, V. Lacoste, H. Pascalis, and J. Pouliquen, Mayaro virus: Complete nucleotide sequence and phylogenetic relationships with other alphaviruses, Virus Research, vol.117, issue.2, 2005.
DOI : 10.1016/j.virusres.2005.11.006

R. Lanciotti, M. Ludwig, E. Rwaguma, J. Lutwama, and T. Kram, Emergence of Epidemic O'nyong-nyong Fever in Uganda after a 35-Year Absence: Genetic Characterization of the Virus, Virology, vol.252, issue.1, pp.258-268, 1998.
DOI : 10.1006/viro.1998.9437

E. Strauss, R. Levinson, C. Rice, J. Dalrymple, and J. Strauss, Nonstructural proteins nsP3 and nsP4 of Ross River and O'Nyong-nyong viruses: Sequence and comparison with those of other alphaviruses, Virology, vol.164, issue.1, pp.265-274, 1988.
DOI : 10.1016/0042-6822(88)90644-7

D. Griffin, Alphaviruses, Fields virology, pp.917-962, 2001.
DOI : 10.1002/0471203076.emm0776

M. Vashishtha, T. Phalen, M. Marquardt, J. Ryu, and A. Ng, A Single Point Mutation Controls the Cholesterol Dependence of Semliki Forest Virus Entry and Exit, The Journal of Cell Biology, vol.1, issue.1, pp.91-99, 1998.
DOI : 10.1073/pnas.77.6.3273

A. Ahn, R. Schoepp, D. Sternberg, and M. Kielian, Growth and Stability of a Cholesterol-Independent Semliki Forest Virus Mutant in Mosquitoes, Virology, vol.262, issue.2, pp.452-456, 1999.
DOI : 10.1006/viro.1999.9932

M. Williams, J. Woodall, P. Corbet, and J. Gillett, O'nyong-nyong fever: An epidemic virus disease in East Africa VIII. Virus isolations from anopheles mosquitoes, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.59, issue.3, pp.300-306, 1965.
DOI : 10.1016/0035-9203(65)90012-X

S. Weaver and A. Barrett, Transmission cycles, host range, evolution and emergence of arboviral disease, Nature Reviews Microbiology, vol.49, issue.10, pp.789-801, 2004.
DOI : 10.1093/jmedent/2.2.203

Y. Lu, T. Cassese, and M. Kielian, The cholesterol requirement for sindbis virus entry and exit and characterization of a spike protein region involved in cholesterol dependence, J Virol, vol.73, pp.4272-4278, 1999.

J. Holland, K. Spindler, F. Horodyski, E. Grabau, and S. Nichol, Rapid evolution of RNA genomes, Science, vol.215, issue.4540, pp.1577-1585, 1982.
DOI : 10.1126/science.7041255

E. Domingo and J. Holland, RNA VIRUS MUTATIONS AND FITNESS FOR SURVIVAL, Annual Review of Microbiology, vol.51, issue.1, pp.151-178, 1997.
DOI : 10.1146/annurev.micro.51.1.151

M. Vignuzzi, J. Stone, J. Arnold, C. Cameron, and R. Andino, Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population, Nature, vol.77, issue.7074, pp.344-348, 2006.
DOI : 10.1128/JVI.77.12.7131-7138.2003

K. Kim, T. Rumenapf, E. Strauss, and J. Strauss, Regulation of Semliki Forest virus RNA replication: A model for the control of alphavirus pathogenesis in invertebrate hosts, Virology, vol.323, pp.153-163, 2004.

C. Heise and D. Kirn, Replication-selective adenoviruses as oncolytic agents, Journal of Clinical Investigation, vol.105, issue.7, pp.847-851, 2000.
DOI : 10.1172/JCI9762
URL : http://www.jci.org/articles/view/9762/files/pdf

M. Heise, L. White, D. Simpson, C. Leonard, and K. Bernard, An Attenuating Mutation in nsP1 of the Sindbis-Group Virus S.A.AR86 Accelerates Nonstructural Protein Processing and Up-Regulates Viral 26S RNA Synthesis, Journal of Virology, vol.77, issue.2, pp.1149-1156, 2003.
DOI : 10.1128/JVI.77.2.1149-1156.2003

M. Suthar, R. Shabman, K. Madric, C. Lambeth, and M. Heise, Identification of Adult Mouse Neurovirulence Determinants of the Sindbis Virus Strain AR86, Journal of Virology, vol.79, issue.7, pp.4219-4228, 2005.
DOI : 10.1128/JVI.79.7.4219-4228.2005

R. Condon and I. Rouse, Acute symptoms and sequelae of Ross River virus infection in South-Western Australia: A follow-up study, Clinical and Diagnostic Virology, vol.3, issue.3, pp.273-284, 1995.
DOI : 10.1016/S0928-0197(94)00043-3

S. Selden and A. Cameron, Changing epidemiology of Ross River virus disease in South Australia, Med J Aust, vol.165, pp.313-317, 1996.

R. Mazaud, J. Salaü-n, H. Montabone, P. Goube, and R. Bazillio, Troubles neurologiques et sensoriels aigus dans la dengue et la fiè vre a ` Chikungunya, Bull Soc Pathol Exot, vol.64, pp.22-30, 1971.

S. Nimmannitya, S. Halstead, S. Cohen, and M. Margiotta, Dengue and chikungunya virus infection in man in Thailand, pp.1962-1964, 1969.