P. W. Ewald, Host-parasite relations, vectors, and the evolution of disease severity, Annu Rev Ecol Syst, vol.14, pp.465-85, 1983.

S. Alizon, A. Hurford, N. Mideo, and M. Van-baalen, Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future, J Evol Biol, vol.22, pp.245-59, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01567938

C. Fraser, T. D. Hollingsworth, R. Chapman, F. De-wolf, and W. P. Hanage, Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis, Proc Natl Acad Sci, vol.104, pp.17441-17447, 2007.

J. C. De-roode, A. J. Yates, and S. Altizer, Virulence-transmission trade-offs and population divergence in virulence in a naturally occurring butterfly parasite, Proc Natl Acad Sci, vol.105, pp.7489-94, 2008.

M. J. Mackinnon, S. Gandon, and A. F. Read, Virulence evolution in response to vaccination: the case of malaria, Vaccine, vol.26, issue.3, pp.42-52, 2008.

D. Ebert and W. W. Weisser, Optimal killing for obligate killers: the evolution of life histories and virulence of semelparous parasites, Proc R Soc B, vol.264, pp.985-91, 1997.

I. Pagán, N. Montes, and M. G. Milgroom, García-Arenal F. Vertical transmission selects for reduced virulence in a plant virus and for increased resistance in the host, PLoS Pathog, vol.10, p.1004293, 2014.

R. M. May and M. A. Nowak, Coinfection and the evolution of parasite virulence, Proc R Soc B, vol.261, pp.209-224, 1995.

J. C. De-roode, R. Pansini, S. J. Cheesman, M. Helinski, S. Huijben et al., Virulence and competitive ability in genetically diverse malaria infections, Proc Natl Acad Sci U S A, vol.102, pp.7624-7632, 2005.

S. P. Brown, D. M. Cornforth, and N. Mideo, Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control, Trends Microbiol, vol.20, pp.336-378, 2012.

M. Boots and A. Sasaki, The evolutionary dynamics of local infection and global reproduction in host-parasite interactions, Ecol Lett, vol.3, pp.181-186, 2000.

J. J. Bull and A. S. Lauring, Theory and empiricism in virulence evolution, PLoS Pathog, vol.10, p.1004387, 2014.

J. J. Bull and D. Ebert, Invasion thresholds and the evolution of nonequilibrium virulence, Evol Appl, vol.1, pp.172-82, 2008.

R. E. Lenski and R. M. May, The evolution of virulence in parasites and pathogens: reconciliation between two competing hypotheses, J Theor Biol, vol.169, pp.253-65, 1994.

E. M. Leroy, B. Kumulungui, X. Pourrut, P. Rouquet, A. Hassanin et al., Fruit bats as reservoirs of Ebola virus, Nature, vol.438, pp.575-581, 2005.

B. Longdon, J. D. Hadfield, J. P. Day, S. Smith, J. E. Mcgonigle et al., The causes and consequences of changes in virulence following pathogen host shifts, PLoS Pathog, vol.11, p.1004728, 2015.

J. Lali?, J. M. Cuevas, and S. F. Elena, Effect of host species on the distribution of mutational fitness effects for an RNA virus, PLoS Genet, vol.7, p.1002378, 2011.

S. Bedhomme, G. Lafforgue, and S. F. Elena, Multihost experimental evolution of a plant RNA virus reveals local adaptation and host-specific mutations, Mol Biol Evol, vol.29, pp.1481-92, 2012.

N. Velasquez, M. J. Hossain, and J. F. Murphy, Differential disease symptoms and fulllength genome sequence analysis for three strains of Tobacco etch virus, Virus Genes, vol.50, pp.442-451, 2015.

F. Revers and J. A. García, Molecular biology of potyviruses, Adv Virus Res, vol.92, pp.101-99, 2015.

M. P. Zwart, A. Willemsen, J. A. Daròs, and S. F. Elena, Experimental evolution of pseudogenization and gene loss in a plant RNA virus, Mol Biol Evol, vol.31, pp.121-155, 2014.

J. C. Carrington, R. Haldeman, V. V. Dolja, and M. A. Restrepo-hartwig, Internal cleavage and trans-proteolytic activities of the VPg-proteinase (NIa) of tobacco etch potyvirus in vivo, J Virol, vol.67, pp.6995-7000, 1993.

M. P. Zwart, J. A. Daròs, and S. F. Elena, One is enough: in vivo effective population size is dose-dependent for a plant RNA virus, PLoS Pathog, vol.7, p.1002122, 2011.

P. Carrasco, J. A. Daròs, P. Agudelo-romero, and S. F. Elena, A real-time RT-PCR assay for quantifying the fitness of Tobacco etch virus in competition experiments, J Virol Methods, vol.139, pp.181-189, 2007.

F. Lab, , 2016.

R. Schmieder and R. Edwards, Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, pp.863-867, 2011.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, pp.357-366, 2012.
DOI : 10.1038/nmeth.1923

URL : http://europepmc.org/articles/pmc3322381?pdf=render

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2087, 2009.

D. C. Koboldt, Q. Zhang, D. E. Larson, D. Shen, M. D. Mclellan et al., VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing, Genome Res, vol.22, pp.568-76, 2012.

. R-core-team, R: A language and environment for statistical computing, 2014.

V. V. Dolja, K. L. Herndon, T. P. Pirone, and J. C. Carrington, Spontaneous mutagenesis of a plant potyvirus genome after insertion of a foreign gene, J Virol, vol.67, pp.5968-75, 1993.

E. Majer, J. A. Daròs, and M. Zwart, Stability and fitness impact of the visually discernible Rosea1 marker in the tobacco etch virus genome, Viruses, vol.5, pp.2153-68, 2013.

C. Plisson, M. Drucker, S. Blanc, S. German-retana, L. Gall et al., Structural characterization of HC-Pro, a plant virus multifunctional protein, J Biol Chem, vol.278, pp.23753-61, 2003.
DOI : 10.1074/jbc.m302512200

URL : https://hal.archives-ouvertes.fr/hal-00108282

Y. M. Shiboleth, E. Haronsky, D. Leibman, T. Arazi, M. Wassenegger et al., The conserved FRNK box in HC-Pro, a plant viral suppressor of gene silencing, is required for small RNA binding and mediates symptom development, J Virol, vol.81, pp.13135-13183, 2007.

J. Sardanyés and S. F. Elena, Error threshold in RNA quasispecies models with complementation, J Theor Biol, vol.265, pp.278-86, 2010.

A. Willemsen, M. P. Zwart, N. Tromas, E. Majer, J. A. Daròs et al., Multiple barriers to the evolution of alternative gene orders in a positive-strand RNA virus, Genetics, vol.202, pp.1503-1524, 2016.

N. Tromas, M. P. Zwart, G. Lafforgue, and S. F. Elena, Within-host spatiotemporal dynamics of plant virus infection at the cellular level, PLoS Genet, vol.10, p.1004186, 2014.
DOI : 10.1371/journal.pgen.1004186

URL : https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1004186&type=printable

A. Willemsen, M. P. Zwart, P. Higueras, J. Sardanyés, and S. F. Elena, Predicting the stability of homologous gene duplications in a plant RNA virus, Genome Biol Evol, vol.8, pp.3065-82, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02004240

D. Vos, M. Dawid, A. Sunderlikova, V. Tans, and S. J. , Breaking evolutionary constraint with a tradeoff ratchet, Proc Natl Acad Sci U S A, vol.112, pp.14906-14917, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01239102

P. Hernández-crespo, S. M. Sait, R. S. Hails, and J. S. Cory, Behavior of a recombinant baculovirus in lepidopteran hosts with different susceptibilities, Appl Environ Microbiol, vol.67, pp.1140-1146, 2001.