V. Olivier, I. Massou, O. Celle, P. Blanchard, F. Schurr et al., In situ hybridization assays for localization of the chronic bee paralysis virus in the honey bee (Apis mellifera) brain, Journal of Virological Methods, vol.153, issue.2, pp.232-237, 2008.
DOI : 10.1016/j.jviromet.2008.06.027

URL : https://hal.archives-ouvertes.fr/hal-00318758

L. Bailey, A. J. Gibbs, and R. D. Woods, The Purification and Properties of Chronic Bee-paralysis Virus, Journal of General Virology, vol.2, issue.2, pp.251-260, 1968.
DOI : 10.1099/0022-1317-2-2-251

R. Thiéry and R. Houlgatte, Molecular characterisation and phylogenetic analysis of Chronic bee paralysis virus, a honey bee virus, Virus Res, vol.132, pp.59-68, 2008.

M. Ribiere, V. Olivier, and P. Blanchard, Chronic bee paralysis: A disease and a virus like no other?, Journal of Invertebrate Pathology, vol.103, pp.120-131, 2010.
DOI : 10.1016/j.jip.2009.06.013

L. Bailey, Viruses Attacking the Honey Bee, In Advances in Virus, vol.20, pp.271-304, 1976.
DOI : 10.1016/S0065-3527(08)60507-2

E. Haubruge, M. Higes, and S. Kasprzak, Phylogenetic analysis of the RNA-dependant RNA polymerase (RdRp) and a predicted structural protein (pSP) of the chronic bee paralysis virus (CBPV) isolated from various geographical regions, Virus Res, vol.144, pp.334-338, 2009.

C. Runckel, M. L. Flenniken, J. C. Engel, J. G. Ruby, D. Ganem et al., Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia, PLoS ONE, vol.35, issue.Pt 6, p.20656, 2011.
DOI : 10.1371/journal.pone.0020656.s009

S. Schuster, F. Zirkel, K. W. Van-cleef, C. Drosten, R. P. Van-rij et al., A Unique Nodavirus with Novel Features: Mosinovirus Expresses Two Subgenomic RNAs, a Capsid Gene of Unknown Origin, and a Suppressor of the Antiviral RNA Interference Pathway, Journal of Virology, vol.88, issue.22, pp.13447-13459, 2014.
DOI : 10.1128/JVI.02144-14

D. B. Kuchibhatla, W. A. Sherman, B. Y. Chung, S. Cook, G. Schneider et al., Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently "Orphan" Viral Proteins, Journal of Virology, vol.88, issue.1, pp.10-20, 2014.
DOI : 10.1128/JVI.02595-13

L. M. Kattenhorn, R. Mills, M. Wagner, A. Lomsadze, V. Makeev et al., Identification of Proteins Associated with Murine Cytomegalovirus Virions, Journal of Virology, vol.78, issue.20, pp.11187-11197, 2004.
DOI : 10.1128/JVI.78.20.11187-11197.2004

P. Renesto, C. Abergel, P. Decloquement, D. Moinier, S. Azza et al., Mimivirus Giant Particles Incorporate a Large Fraction of Anonymous and Unique Gene Products, Journal of Virology, vol.80, issue.23, pp.11678-11685, 2006.
DOI : 10.1128/JVI.00940-06

URL : https://hal.archives-ouvertes.fr/hal-00165618

R. Wang, F. Deng, D. Hou, Y. Zhao, L. Guo et al., Proteomics of the Autographa californica Nucleopolyhedrovirus Budded Virions, Journal of Virology, vol.84, issue.14, pp.7233-7242, 2010.
DOI : 10.1128/JVI.00040-10

R. Zeng, H. Q. Ruan, X. S. Jiang, H. Zhou, L. Shi et al., Proteomic Analysis of SARS Associated Coronavirus Using Two-Dimensional Liquid Chromatography Mass Spectrometry and One-Dimensional Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis Followed by Mass Spectroemtric Analysis, Journal of Proteome Research, vol.3, issue.3, pp.549-555, 2004.
DOI : 10.1021/pr034111j

E. Chertova, O. Chertov, L. V. Coren, J. D. Roser, C. M. Trubey et al., Proteomic and Biochemical Analysis of Purified Human Immunodeficiency Virus Type 1 Produced from Infected Monocyte-Derived Macrophages, Journal of Virology, vol.80, issue.18, pp.9039-9052, 2006.
DOI : 10.1128/JVI.01013-06

P. Blanchard, M. Ribière, O. Celle, P. Lallemand, F. Schurr et al., Evaluation of a real-time two-step RT-PCR assay for quantitation of Chronic bee paralysis virus (CBPV) genome in experimentally-infected bee tissues and in life stages of a symptomatic colony, Journal of Virological Methods, vol.141, issue.1, pp.7-13, 2007.
DOI : 10.1016/j.jviromet.2006.11.021

URL : https://hal.archives-ouvertes.fr/anses-00414768

P. Blanchard, J. Regnault, F. Schurr, E. Dubois, and M. Ribière, Intra-laboratory validation of chronic bee paralysis virus quantitation using an accredited standardised real-time quantitative RT-PCR method, Journal of Virological Methods, vol.180, issue.1-2, pp.26-31, 2012.
DOI : 10.1016/j.jviromet.2011.12.005

T. Bakonyi, E. Grabensteiner, J. Kolodziejek, M. Rusvai, G. Topolska et al., Phylogenetic Analysis of Acute Bee Paralysis Virus Strains, Applied and Environmental Microbiology, vol.68, issue.12, pp.6446-6450, 2002.
DOI : 10.1128/AEM.68.12.6446-6450.2002

D. L. Cox-foster, S. Conlan, E. C. Holmes, G. Palacios, J. D. Evans et al., A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder, Science, vol.318, issue.5848, pp.283-287, 2007.
DOI : 10.1126/science.1146498

E. Grabensteiner, W. Ritter, M. J. Carter, S. Davison, H. Pechhacker et al., Sacbrood Virus of the Honeybee (Apis mellifera): Rapid Identification and Phylogenetic Analysis Using Reverse Transcription-PCR, Clinical and Vaccine Immunology, vol.8, issue.1, pp.93-104, 2001.
DOI : 10.1128/CDLI.8.1.93-104.2001

O. H. Lowry, A. L. Rosebrough, N. J. Farr, and R. J. Randall, Protein measurement with the Folin-Phenol reagents, J. Biol. Chem, vol.193, pp.265-275, 1951.

V. Lantez, K. Dalle, R. Charrel, C. Baronti, B. Canard et al., Comparative Production Analysis of Three Phlebovirus Nucleoproteins under Denaturing or Non-Denaturing Conditions for Crystallographic Studies, PLoS Neglected Tropical Diseases, vol.83, issue.1, p.936, 2011.
DOI : 10.1371/journal.pntd.0000936.s001

M. Ribiere, J. P. Faucon, and M. Pépin, L.) paralysis virus infection: application to a field survey, Apidologie, vol.31, issue.5, pp.567-577, 2000.
DOI : 10.1051/apido:2000147

URL : https://hal.archives-ouvertes.fr/hal-00280707

. Protparam, Available online: http://web.expasy.org/protparam (accessed on 20, 2015.

J. Kyte and R. F. Doolittle, A simple method for displaying the hydropathic character of a protein, Journal of Molecular Biology, vol.157, issue.1, pp.105-132, 1982.
DOI : 10.1016/0022-2836(82)90515-0

D. T. Jones, Protein secondary structure prediction based on position-specific scoring matrices, Journal of Molecular Biology, vol.292, issue.2, pp.195-202, 1999.
DOI : 10.1006/jmbi.1999.3091

J. Söndig, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, pp.951-960, 2005.

A. V. Kochentov, A. Palyanov, I. Titov, D. Grigorovich, A. Sarai et al., AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site, BMC Bioinformatics, vol.8, issue.1, p.318, 2007.
DOI : 10.1186/1471-2105-8-318

A. M. Waterhouse, J. B. Procter, D. M. Martin, M. Clamp, and G. J. Barton, Jalview Version 2--a multiple sequence alignment editor and analysis workbench, Bioinformatics, vol.25, issue.9, pp.1189-1191, 2009.
DOI : 10.1093/bioinformatics/btp033

S. Cook, B. Y. Chung, D. Bass, G. Moureau, S. Tang et al., Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts, PLoS ONE, vol.27, issue.11, p.80720, 2013.
DOI : 10.1371/journal.pone.0080720.t001

N. X. Fang, I. H. Frazer, J. Zhou, and G. J. Fernando, Post translational modifications of recombinant human Papillomavirus type 6b major capsid protein, Virus Research, vol.60, issue.2, pp.113-121, 1999.
DOI : 10.1016/S0168-1702(98)00117-8

U. Geigenmuller, N. H. Ginzton, and S. M. Matsui, Studies on intracellular processing of the capsid protein of human astrovirus serotype 1 in infected cells, Journal of General Virology, vol.83, issue.7, pp.1691-1695, 2002.
DOI : 10.1099/0022-1317-83-7-1691

A. I. Soldevila, S. Huang, and S. A. Ghabrial, Assembly of the Hv190S Totivirus Capsid Is Independent of Posttranslational Modification of the Capsid Protein, Virology, vol.251, issue.2, pp.327-333, 1998.
DOI : 10.1006/viro.1998.9443

Z. Knejzlík, M. Strohalm, L. Sedlácková, M. Kodícek, M. Sakalian et al., Isolation and characterization of the Mason???Pfizer monkey virus p12 protein, Virology, vol.324, issue.1, pp.204-212, 2004.
DOI : 10.1016/j.virol.2004.03.023

S. Curry, E. Fry, W. Blakemore, R. Abu-ghazaleh, T. Jackson et al., Dissecting the roles of VP0 cleavage and RNA packaging in picornavirus capsid stabilization: The structure of empty capsids of foot-and-mouth disease virus, J. Virol, vol.71, pp.9743-9752, 1997.

R. Basavappa, R. Syed, O. Flore, J. P. Icenogle, D. J. Filman et al., Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: Structure of the empty capsid assembly intermediate at 2.9 ?? resolution, Protein Science, vol.35, issue.10, pp.1651-1669, 1994.
DOI : 10.1002/pro.5560031005

T. M. Gallagher and R. R. Rueckert, Assembly-dependent maturation cleavage in provirions of a small icosahedral insect ribovirus, J. Virol, vol.62, pp.3399-3406, 1988.

M. Kozak, Pushing the limits of the scanning mechanism for initiation of translation, Gene, vol.299, issue.1-2, pp.1-34, 2002.
DOI : 10.1016/S0378-1119(02)01056-9

K. Clyde and E. Harris, RNA Secondary Structure in the Coding Region of Dengue Virus Type 2 Directs Translation Start Codon Selection and Is Required for Viral Replication, Journal of Virology, vol.80, issue.5, pp.2170-2182, 2006.
DOI : 10.1128/JVI.80.5.2170-2182.2006

R. Tan and A. D. Frankel, Structural variety of arginine-rich RNA-binding peptides., Proc. Natl. Acad. Sci, pp.5282-5286, 1995.
DOI : 10.1073/pnas.92.12.5282

A. L. Rao and G. L. Grantham, Molecular Studies on Bromovirus Capsid Protein, Virology, vol.226, issue.2, pp.294-305, 1996.
DOI : 10.1006/viro.1996.0657

URL : http://doi.org/10.1006/viro.1997.8579

Y. G. Choi, G. L. Grantham, and A. L. Rao, Molecular Studies on Bromovirus Capsid Protein, Virology, vol.270, issue.2, pp.377-385, 2000.
DOI : 10.1006/viro.2000.0312

P. A. Venter, D. Marshall, and A. Schneemann, Dual Roles for an Arginine-Rich Motif in Specific Genome Recognition and Localization of Viral Coat Protein to RNA Replication Sites in Flock House Virus-Infected Cells, Journal of Virology, vol.83, issue.7, pp.2872-2882, 2009.
DOI : 10.1128/JVI.01780-08

S. H. Park, T. L. Sit, K. H. Kim, and S. A. Lommel, The Red clover necrotic mosaic virus capsid protein N-terminal lysine-rich motif is a determinant of symptomatology and virion accumulation, Molecular Plant Pathology, vol.13, issue.7, pp.744-754, 2012.
DOI : 10.1111/j.1364-3703.2011.00784.x

M. Banerjee and J. E. Johnson, Activation, Exposure and Penetration of Virally Encoded, Membrane-Active Polypeptides During Non enveloped Virus Entry, Curr. Protein Pept. Sci, vol.9, pp.16-27, 2008.
DOI : 10.2174/9781608054879113010007

A. Chevin, F. Schurr, P. Blanchard, R. Thiéry, and M. Ribière, Experimental infection of the honeybee (Apis mellifera L.) with the chronic bee paralysis virus (CBPV): infectivity of naked CBPV RNAs, Virus Research, vol.167, issue.2, pp.173-178, 2012.
DOI : 10.1016/j.virusres.2012.04.012

I. Youssef, F. Schurr, A. Goulet, N. Cougoule, R. Thiéry et al., RNA 1 and RNA 2 genomic segments of Chronic Bee Paralysis Virus (CBPV) are sufficient to recover an infectious virus, J. Immun. Res