Mechanisms of Hepatitis C Viral Resistance to Direct Acting Antivirals, Viruses, vol.62, issue.12, pp.6716-6729, 2015. ,
DOI : 10.1016/j.antiviral.2014.02.011
Inferring viral quasispecies spectra from 454 pyrosequencing reads, BMC Bioinformatics, vol.12, issue.Suppl 6, p.1, 2011. ,
DOI : 10.1016/j.meegid.2009.07.011
Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data, Frontiers in Microbiology, vol.3, p.329, 2012. ,
DOI : 10.3389/fmicb.2012.00329
Within-Host Dynamics of the Hepatitis C Virus Quasispecies Population in HIV-1/HCV Coinfected Patients, PLoS ONE, vol.23, issue.Suppl 1, p.16551, 2011. ,
DOI : 10.1371/journal.pone.0016551.s004
Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection, PLoS Pathogens, vol.7, issue.9, p.1002243, 2011. ,
DOI : 10.1371/journal.ppat.1002243.s012
How does adaptation sweep through the genome? Insights from long-term selection experiments, Proceedings of the Royal Society B: Biological Sciences, vol.7, issue.7291, pp.2795029-2795067, 1749. ,
DOI : 10.1038/nature08923
QIIME allows analysis of high-throughput community sequencing data, Nature Methods, vol.8, issue.5, pp.335-336, 2010. ,
DOI : 10.1038/nmeth.f.303
Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, vol.25, issue.11, pp.251422-251425, 2009. ,
DOI : 10.1093/bioinformatics/btp163
Intra-host evolution of multiple genotypes of hepatitis C virus in a chronically infected patient with HIV along a 13-year follow-up period, Virology, vol.449, pp.449317-327, 2014. ,
DOI : 10.1016/j.virol.2013.11.034
jModelTest 2: more models, new heuristics and parallel computing, Nature Methods, vol.9, issue.8, pp.772-772, 2012. ,
DOI : 10.1109/TAC.1974.1100705
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences, Molecular Biology and Evolution, vol.22, issue.5, pp.1185-1192, 2005. ,
DOI : 10.1093/molbev/msi103
Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Molecular Biology and Evolution, vol.29, issue.8, pp.1969-1973, 2012. ,
DOI : 10.1093/molbev/mss075
Molecular quasi-species, The Journal of Physical Chemistry, vol.92, issue.24, pp.6881-6891, 1988. ,
DOI : 10.1021/j100335a010
The Outcome of Acute Hepatitis C Predicted by the Evolution of the Viral Quasispecies, Science, vol.288, issue.5464, pp.288339-288383, 2000. ,
DOI : 10.1126/science.288.5464.339
More effective drugs lead to harder selective sweeps in the evolu- CHAPITRE 2, DYNAMIQUE DE L'ÉVOLUTION INTRA-PATIENT DU VHC PAR NGS52 tion of drug resistance in HIV-1. eLife, 2016. ,
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-224, 2010. ,
DOI : 10.1093/molbev/msp259
URL : https://hal.archives-ouvertes.fr/lirmm-00511794
A New Evolutionary Model for Hepatitis C Virus Chronic Infection, PLoS Pathogens, vol.22, issue.5, p.1002656, 2012. ,
DOI : 10.1371/journal.ppat.1002656.g001
The mode and tempo of hepatitis C virus evolution within and among hosts, BMC Evolutionary Biology, vol.54, issue.Suppl 1, p.131, 2011. ,
DOI : 10.1128/AAC.00556-10
Ultra-Deep Pyrosequencing (UDPS) Data Treatment to Study Amplicon HCV Minor Variants, PLoS ONE, vol.19, issue.12, p.83361, 2013. ,
DOI : 10.1371/journal.pone.0083361.s003
Viral quasispecies complexity measures, Virology, vol.493, pp.227-237, 2016. ,
DOI : 10.1016/j.virol.2016.03.017
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
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010. ,
DOI : 10.1093/sysbio/syq010
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study, Virus Evolution, vol.2, issue.1, 2016. ,
DOI : 10.1093/ve/vew003
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, Journal of Molecular Evolution, vol.275, issue.3, pp.160-174, 1985. ,
DOI : 10.1016/B978-1-4832-2734-4.50017-6
Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection, PLoS Pathogens, vol.4, issue.3, 2012. ,
DOI : 10.1371/journal.ppat.1002529.s001
Soft Sweeps: Molecular Population Genetics of Adaptation From Standing Genetic Variation, Genetics, vol.169, issue.4, pp.2335-52, 2005. ,
DOI : 10.1534/genetics.104.036947
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, vol.30, issue.4, pp.772-780, 2013. ,
DOI : 10.1093/molbev/mst010
The Los Alamos hepatitis C sequence database, Bioinformatics, vol.21, issue.3, pp.379-384, 2005. ,
DOI : 10.1093/bioinformatics/bth485
Naturally Occurring Resistance-Associated Variants of Hepatitis C Virus Protease Inhibitors in Poor Responders to Pegylated Interferon-Ribavirin, Journal of Clinical Microbiology, vol.53, issue.7, 2015. ,
DOI : 10.1128/JCM.03633-14
URL : https://hal.archives-ouvertes.fr/hal-01243613
Ultradeep Pyrosequencing of NS3 To Predict Response to Triple Therapy with Protease Inhibitors in Previously Treated Chronic Hepatitis C Patients, Journal of Clinical Microbiology, vol.53, issue.2, pp.389-397, 2015. ,
DOI : 10.1128/JCM.02547-14
URL : https://hal.archives-ouvertes.fr/hal-01132344
Analysis of Hepatitis C Virus Intrahost Diversity across the Coding Region by Ultradeep Pyrosequencing, Journal of Virology, vol.86, issue.7, pp.3952-3960, 2012. ,
DOI : 10.1128/JVI.06627-11
The role of mutational robustness in RNA virus evolution, Nature Reviews Microbiology, vol.79, issue.5, pp.327-336, 2013. ,
DOI : 10.1128/JVI.79.18.11555-11558.2005
Inter and intrapatient evolution of hepatitis C virus, Annals of Hepatology, vol.14, issue.4, pp.442-449, 2015. ,
Genetic Diversity of Near Genome-Wide Hepatitis C Virus Sequences during Chronic Infection: Evidence for Protein Structural Conservation Over Time, PLoS ONE, vol.104, issue.Pt 5, 2011. ,
DOI : 10.1371/journal.pone.0019562.s004
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, vol.17, issue.1, p.10, 2011. ,
DOI : 10.14806/ej.17.1.200
The hitch-hiking effect of a favourable gene, Genetical Research, vol.19, issue.01, pp.23-35, 1974. ,
DOI : 10.1038/2191114a0
Population genomics of rapid adaptation by soft selective sweeps, Trends in Ecology & Evolution, vol.28, issue.11, pp.659-669, 2013. ,
DOI : 10.1016/j.tree.2013.08.003
Within-host nucleotide diversity of virus populations: Insights from next-generation sequencing, Infection, Genetics and Evolution, vol.30, pp.1-7, 2015. ,
DOI : 10.1016/j.meegid.2014.11.026
pegas: an R package for population genetics with an integrated-modular approach, Bioinformatics, vol.26, issue.3, pp.419-420, 2010. ,
DOI : 10.1093/bioinformatics/btp696
Review: Therapeutic implications of hepatitis C virus resistance to antiviral drugs, Therapeutic advances in gastroenterology, pp.205-224, 2009. ,
DOI : 10.1074/jbc.M610207200
Loss and Recovery of Genetic Diversity in Adapting Populations of HIV, PLoS Genetics, vol.69, issue.1, p.1004000, 2014. ,
DOI : 10.1371/journal.pgen.1004000.s008
Standing Genetic Variation and the Evolution of Drug Resistance in HIV, PLoS Computational Biology, vol.330, issue.6, p.1002527, 2012. ,
DOI : 10.1371/journal.pcbi.1002527.s003
High prevalence of Hepatitis C virus genotype 6 in Vietnam, 2009. ,
R : A Language and Environment for Statistical Computing, 2016. ,
Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection, PLOS Pathogens, vol.191, issue.2, p.1005894, 2016. ,
DOI : 10.1371/journal.ppat.1005894.s014
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen), Virus Evolution, vol.2, issue.1, p.7, 2016. ,
DOI : 10.1093/ve/vew007
Temporal Variations in the Hepatitis C Virus Intrahost Population during Chronic Infection, Journal of Virology, vol.85, issue.13, pp.6369-6380, 2011. ,
DOI : 10.1128/JVI.02204-10
Compartmentalization of Hepatitis C Virus Genotypes between Plasma and Peripheral Blood Mononuclear Cells, Journal of Virology, vol.79, issue.10, pp.796349-6357, 2005. ,
DOI : 10.1128/JVI.79.10.6349-6357.2005
The neighbor-joining method : a new method for reconstructing phylogenetic trees, Molecular biology and evolution, vol.4, issue.4, pp.406-431, 1987. ,
Determining hepatitis C genotype by analyzing the sequence of the NS5b region, Journal of Virological Methods, vol.109, issue.2, pp.187-193, 2003. ,
DOI : 10.1016/S0166-0934(03)00070-3
Multiple infections with different HCV genotypes: prevalence and clinical impact, Journal of Clinical Virology, vol.27, issue.2, pp.200-204, 2003. ,
DOI : 10.1016/S1386-6532(02)00264-0
Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes, Hepatology, vol.17, issue.4, pp.962-973, 2005. ,
DOI : 10.1099/0022-1317-82-5-1001
URL : https://hal.archives-ouvertes.fr/hal-00313678
Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: Updated criteria and genotype assignment web resource, Hepatology, vol.28, issue.244, pp.318-327, 2014. ,
DOI : 10.1002/jmv.23300
Fast Dating Using Least-Squares Criteria and Algorithms, Systematic Biology, vol.65, issue.1, pp.82-97, 2016. ,
DOI : 10.1093/sysbio/syv068
URL : https://hal.archives-ouvertes.fr/lirmm-01348367
The role of resistance in HCV treatment, Best Practice & Research Clinical Gastroenterology, vol.26, issue.4, pp.487-503, 2012. ,
DOI : 10.1016/j.bpg.2012.09.011
Hepatitis C Virus Transmission Bottlenecks Analyzed by Deep Sequencing, Journal of Virology, vol.84, issue.12, pp.6218-6228, 2010. ,
DOI : 10.1128/JVI.02271-09
De novo assembly of highly diverse viral populations, BMC Genomics, vol.13, issue.1, p.475, 2012. ,
DOI : 10.1084/jem.20090378
Genetic Diversity of Near Genome-Wide Hepatitis C Virus Sequences during Chronic Infection: Evidence for Protein Structural Conservation Over Time, PLoS ONE, vol.104, issue.Pt 5, p.19562, 2011. ,
DOI : 10.1371/journal.pone.0019562.s004
Hepatitis C virus infection, Nature Reviews Disease Primers, vol.64, p.17006, 2017. ,
DOI : 10.1111/j.1872-034X.2007.00053.x
Mathematical model for studying genetic variation in terms of restriction endonucleases., Proceedings of the National Academy of Sciences, pp.765269-5273, 1979. ,
DOI : 10.1073/pnas.76.10.5269
Within-host nucleotide diversity of virus populations: Insights from next-generation sequencing, Infection, Genetics and Evolution, vol.30, pp.1-7, 2015. ,
DOI : 10.1016/j.meegid.2014.11.026
What is a quasispecies ? Trends in Ecology & Evolution, pp.118-121, 1992. ,
Extinction of Hepatitis C Virus by Ribavirin in Hepatoma Cells Involves Lethal Mutagenesis, PLoS ONE, vol.510, issue.8, p.71039, 2013. ,
DOI : 10.1371/journal.pone.0071039.s008
Hepatitis C Virus Resistance to Direct-Acting Antiviral Drugs in??Interferon-Free Regimens, Gastroenterology, vol.151, issue.1, pp.70-86, 2016. ,
DOI : 10.1053/j.gastro.2016.04.003
Ebi : Next generation sequencing practical course, 2012. ,
Temporal Variations in the Hepatitis C Virus Intrahost Population during Chronic Infection, Journal of Virology, vol.85, issue.13, pp.856369-6380, 2011. ,
DOI : 10.1128/JVI.02204-10
Fast Dating Using Least-Squares Criteria and Algorithms, Systematic Biology, vol.65, issue.1, pp.82-97, 2015. ,
DOI : 10.1093/sysbio/syv068
URL : https://hal.archives-ouvertes.fr/lirmm-01348367