Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries, Genome Biology, vol.12, issue.2, pp.18-28, 2011. ,
DOI : 10.1093/bioinformatics/btp324
Rapid next-generation sequencing of dengue, EV-A71 and RSV-A viruses, Journal of Virological Methods, vol.226, pp.7-14, 2015. ,
DOI : 10.1016/j.jviromet.2015.09.004
Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR, BMC Molecular Biology, vol.9, issue.1, pp.77-87, 2008. ,
DOI : 10.1186/1471-2199-9-77
Characterization of the genome of human enteroviruses: Design of generic primers for amplification and sequencing of different regions of the viral genome, Journal of Virological Methods, vol.149, issue.2, pp.277-284, 2008. ,
DOI : 10.1016/j.jviromet.2008.01.027
URL : https://hal.archives-ouvertes.fr/pasteur-00318628
Genetic Relationship between Cocirculating Human Enteroviruses Species C, PLoS ONE, vol.6, issue.Pt 10, 2011. ,
DOI : 10.1371/journal.pone.0024823.t001
URL : https://hal.archives-ouvertes.fr/pasteur-00835576
Isolation and characterization of enteroviruses from clinical samples Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region, Methods Mol. Biol. 1387 J. Virol, vol.77, pp.19-28, 2003. ,
Molecular strategy for ???serotyping??? of human enteroviruses, Journal of General Virology, vol.82, issue.1, pp.79-91, 2001. ,
DOI : 10.1099/0022-1317-82-1-79
Recombination between Poliovirus and Coxsackie A Viruses of Species C: A Model of Viral Genetic Plasticity and Emergence, Viruses, vol.3, issue.12, pp.1460-1484, 2011. ,
DOI : 10.3390/v3081460
The cis-acting replication elements define human enterovirus and rhinovirus species, RNA, vol.14, issue.8, pp.1568-1578, 2008. ,
DOI : 10.1261/rna.1031408
Targeted full-genome amplification and sequencing of dengue virus types 1???4 from South America, Journal of Virological Methods, vol.235, pp.158-167, 2016. ,
DOI : 10.1016/j.jviromet.2016.06.001
URL : https://hal.archives-ouvertes.fr/hal-01445723
Viral genome sequencing by random priming methods, BMC Genomics, vol.9, issue.1, pp.5-10, 2008. ,
DOI : 10.1186/1471-2164-9-5
Preferential Amplification of Pathogenic Sequences, Scientific Reports, vol.79, 2015. ,
DOI : 10.1038/srep11047
Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery, Journal of Virological Methods, vol.195, pp.194-204, 2014. ,
DOI : 10.1016/j.jviromet.2013.08.035
Library construction for next-generation sequencing: Overviews and challenges, BioTechniques, vol.56, issue.2, pp.61-77, 2014. ,
DOI : 10.2144/000114133
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351865
Complete coding regions of the prototypes enterovirus B93 and C95: Phylogenetic analyses of the P1 and P3 regions of EV-B and EV-C strains, Journal of Medical Virology, vol.271, issue.3, pp.485-497, 2015. ,
DOI : 10.1002/jmv.24062
Picornaviridae, Ninth Report of the International Committee on Taxonomy of Viruses, pp.855-880, 2012. ,
Recombination among human non-polio enteroviruses: implications for epidemiology and evolution, Virus Genes, vol.9, issue.Pt 10, pp.177-188, 2015. ,
DOI : 10.1007/s11262-014-1152-y
Quantification of enterovirus RNA in sludge samples using single tube real-time RT-PCR Available online at: http://www, Enterovirus-RNA-in-Sludge-Samples-Using-Single-Tube- Real-Time-RT-PCR/biotechniques-44174.html, pp.88-93, 2000. ,
Using the Basic Local Alignment Search Tool (BLAST). CSH Protoc, 2007. ,
Within-host nucleotide diversity of virus populations: Insights from next-generation sequencing, Infection, Genetics and Evolution, vol.30, 2015. ,
DOI : 10.1016/j.meegid.2014.11.026
Sensitive, Seminested PCR Amplification of VP1 Sequences for Direct Identification of All Enterovirus Serotypes from Original Clinical Specimens, Journal of Clinical Microbiology, vol.44, issue.8, pp.2698-2704, 2006. ,
DOI : 10.1128/JCM.00542-06
Non-random DNA fragmentation in next-generation sequencing, Scientific Reports, vol.324, 2014. ,
DOI : 10.1038/srep04532
Co-Circulation and Evolution of Polioviruses and Species C Enteroviruses in a District of Madagascar, PLoS Pathogens, vol.229, issue.12, 2007. ,
DOI : 10.1371/journal.ppat.0030191.sg001
URL : https://hal.archives-ouvertes.fr/pasteur-00318673
High Frequency of Human Enterovirus Species C Circulation in Madagascar, Journal of Clinical Microbiology, vol.43, issue.1, pp.242-249, 2005. ,
DOI : 10.1128/JCM.43.1.242-249.2005
URL : https://hal.archives-ouvertes.fr/pasteur-00319480
The origin of biased sequence depth in sequenceindependent nucleic acid amplification and optimization for efficient massive parallel sequencing, PLoS ONE, vol.8, 2013. ,
High Frequency and Diversity of Species C Enteroviruses in Cameroon and Neighboring Countries, Journal of Clinical Microbiology, vol.51, issue.3, pp.759-770, 1128. ,
DOI : 10.1128/JCM.02119-12
Mechanisms of genetic variation in polioviruses, Reviews in Medical Virology, vol.101, issue.(Suppl 1), pp.358-371, 2010. ,
DOI : 10.1002/rmv.663
Picornavirus and enterovirus diversity with associated human diseases, Infection, Genetics and Evolution, vol.14, 2013. ,
DOI : 10.1016/j.meegid.2012.10.016
Comparison of next generation sequencing technologies for the comprehensive assessment of full-length hepatitis C viral genomes, J. Clin. Microbiol, 2016. ,
Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C, Journal of General Virology, vol.94, issue.Pt_9, 1995. ,
DOI : 10.1099/vir.0.053462-0
Library preparation methods for next-generation sequencing: Tone down the bias, Experimental Cell Research, vol.322, issue.1, 2014. ,
DOI : 10.1016/j.yexcr.2014.01.008
Beyond the Consensus: Dissecting Within-Host Viral Population Diversity of Foot-and-Mouth Disease Virus by Using Next-Generation Genome Sequencing, Journal of Virology, vol.85, issue.5, pp.2266-2275, 1128. ,
DOI : 10.1128/JVI.01396-10
Poliovirus Laboratory Based Surveillance: An Overview, Methods Mol. Biol, vol.210, issue.Suppl 1, pp.11-18, 2016. ,
DOI : 10.1007/978-1-4939-3292-4_2