G. M. Allan and J. A. Ellis, Porcine Circoviruses: A Review, Journal of Veterinary Diagnostic Investigation, vol.141, issue.1, pp.3-14, 2000.
DOI : 10.1099/0022-1317-78-1-221

C. N. Bernstein, G. Nayar, A. Hamel, and J. F. Blanchard, Study of Animal-Borne Infections in the Mucosas of Patients with Inflammatory Bowel Disease and Population-Based Controls, Journal of Clinical Microbiology, vol.41, issue.11, pp.4986-4990, 2003.
DOI : 10.1128/JCM.41.11.4986-4990.2003

P. Biagini, Anellovirus, Virus taxonomy. Eighth report of the International Committee on Taxonomy of Viruses, pp.335-341, 2005.
DOI : 10.1016/B978-012374410-4.00694-4
URL : https://hal.archives-ouvertes.fr/halshs-00637762

P. Biagini, Classification of TTV and Related Viruses (Anelloviruses), 2009.
DOI : 10.1007/978-3-540-70972-5_2
URL : https://hal.archives-ouvertes.fr/halshs-00637837

O. Blinkova, J. Victoria, Y. Li, B. Keele, C. Sanz et al., Novel circular DNA viruses in stool samples of wild-living chimpanzees, Journal of General Virology, vol.91, issue.1, pp.74-96, 2010.
DOI : 10.1099/vir.0.015446-0

A. K. Cheung, Rolling-Circle Replication of an Animal Circovirus Genome in a Theta-Replicating Bacterial Plasmid in Escherichia coli, Journal of Virology, vol.80, issue.17, pp.8686-8694, 2006.
DOI : 10.1128/JVI.00655-06

S. Duffy, L. A. Shackelton, and E. C. Holmes, Rates of evolutionary change in viruses: patterns and determinants, Nature Reviews Genetics, vol.79, issue.4, pp.267-276, 2008.
DOI : 10.1038/nrg2323

J. A. Ellis, C. Konoby, K. H. West, G. M. Allan, S. Krakowka et al., Lack of antibodies to porcine circovirus type 2 virus in beef and dairy cattle and horses in western Canada, Can. Vet. J, vol.42, pp.461-464, 2001.

O. Garkavenko, M. C. Croxson, M. Irgang, A. Karlas, J. Denner et al., Monitoring for Presence of Potentially Xenotic Viruses in Recipients of Pig Islet Xenotransplantation, Journal of Clinical Microbiology, vol.42, issue.11, pp.5353-5356, 2004.
DOI : 10.1128/JCM.42.11.5353-5356.2004

M. J. Gibbs, V. V. Smeianov, J. L. Steele, P. Upcroft, and B. A. Efimov, Two Families of Rep-Like Genes That Probably Originated by Interspecies Recombination Are Represented in Viral, Plasmid, Bacterial, and Parasitic Protozoan Genomes, Molecular Biology and Evolution, vol.23, issue.6, pp.1097-1100, 2006.
DOI : 10.1093/molbev/msj122

S. Guindon and O. Gascuel, 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

M. Y. Halami, H. Nieper, H. Muller, and R. Johne, Detection of a novel circovirus in mute swans (Cygnus olor) by using nested broad-spectrum PCR, Virus Research, vol.132, issue.1-2, pp.208-212, 2008.
DOI : 10.1016/j.virusres.2007.11.001

K. Hattermann, A. Maerz, H. Slanina, C. Schmitt, and A. Mankertz, Assessing the risk potential of porcine circoviruses for xenotransplantation: consensus primer-PCR-based search for a human circovirus, Xenotransplantation, vol.217, issue.6, pp.547-550, 2004.
DOI : 10.1111/j.1399-3089.2004.00134.x

K. Hattermann, C. Roedner, C. Schmitt, T. Finsterbusch, T. Steinfeldt et al., Infection studies on human cell lines with porcine circovirus type 1 and porcine circovirus type 2, Xenotransplantation, vol.217, issue.3, pp.284-294, 2004.
DOI : 10.1128/JVI.76.18.9434-9445.2002

K. Hattermann, C. Schmitt, D. Soike, and A. Mankertz, Cloning and sequencing of Duck circovirus (DuCV), Archives of Virology, vol.148, issue.12, pp.2471-2480, 2003.
DOI : 10.1007/s00705-003-0181-y

R. Johne, D. Fernandez-de-luco, U. Hofle, and H. Muller, Genome of a novel circovirus of starlings, amplified by multiply primed rolling-circle amplification, Journal of General Virology, vol.87, issue.5, pp.1189-1195, 2006.
DOI : 10.1099/vir.0.81561-0

R. Johne, R. Raue, C. Grund, E. F. Kaleta, and H. Muller, Recombinant expression of a truncated capsid protein of beak and feather disease virus and its application in serological tests, Avian Pathology, vol.52, issue.3, pp.328-336, 2004.
DOI : 10.1016/S0378-1135(99)00070-X

S. Kumar, M. Nei, J. Dudley, and K. Tamura, MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences, Briefings in Bioinformatics, vol.9, issue.4, pp.299-306, 2008.
DOI : 10.1093/bib/bbn017

P. Lefeuvre, J. M. Lett, A. Varsani, and D. P. Martin, Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses, Journal of Virology, vol.83, issue.6, pp.2697-2707, 2009.
DOI : 10.1128/JVI.02152-08
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648288

. Alcami, High diversity of the viral community from an Antarctic lake, Science, vol.326, pp.858-861, 2009.

A. Mankertz, R. Caliskan, K. Hattermann, B. Hillenbrand, P. Kurzendoerfer et al., Molecular biology of Porcine circovirus: analyses of gene expression and viral replication, Veterinary Microbiology, vol.98, issue.2, pp.81-88, 2004.
DOI : 10.1016/j.vetmic.2003.10.014

A. Mankertz, K. Hattermann, B. Ehlers, and D. Soike, Cloning and sequencing of columbid circovirus (CoCV), a new circovirus from pigeons, Archives of Virology, vol.145, issue.12, pp.2469-2479, 2000.
DOI : 10.1007/s007050070002

A. Manning, S. J. Willey, J. E. Bell, and P. Simmonds, Comparison of Tissue Distribution, Persistence, and Molecular Epidemiology of Parvovirus B19 and Novel Human Parvoviruses PARV4 and Human Bocavirus, The Journal of Infectious Diseases, vol.195, issue.9, pp.1345-1352, 2007.
DOI : 10.1086/513280

G. P. Nayar, A. L. Hamel, L. Lin, C. Sachvie, E. Grudeski et al., Evidence for circovirus in cattle with respiratory disease and from aborted bovine fetuses, Can. Vet. J, vol.40, pp.277-278, 1999.

T. F. Ng, C. Manire, K. Borrowman, T. Langer, L. Ehrhart et al., Discovery of a Novel Single-Stranded DNA Virus from a Sea Turtle Fibropapilloma by Using Viral Metagenomics, Journal of Virology, vol.83, issue.6, pp.2500-2509, 2009.
DOI : 10.1128/JVI.01946-08

F. D. Niagro, A. N. Forsthoefel, R. P. Lawther, L. Kamalanathan, B. W. Ritchie et al., Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses, Archives of Virology, vol.143, issue.9, pp.1723-1744, 1998.
DOI : 10.1007/s007050050412

P. Norja, K. Hokynar, L. M. Aaltonen, R. Chen, A. Ranki et al., Bioportfolio: Lifelong persistence of variant and prototypic erythrovirus DNA genomes in human tissue, Proc. Natl. Acad. Sci. U. S. A, pp.7450-7453, 2006.
DOI : 10.1073/pnas.0602259103

M. H. Noteborn, G. F. De-boer, D. J. Van-roozelaar, C. Karreman, O. Kranenburg et al., Characterization of cloned chicken anemia virus DNA that contains all elements for the infectious replication cycle, J. Virol, vol.65, pp.3131-3139, 1991.

T. Opriessnig, X. J. Meng, and P. G. Halbur, Porcine Circovirus Type 2???Associated Disease: Update on Current Terminology, Clinical Manifestations, Pathogenesis, Diagnosis, and Intervention Strategies, Journal of Veterinary Diagnostic Investigation, vol.123, issue.6, pp.591-615, 2007.
DOI : 10.1177/104063879901100608

T. Opriessnig, A. R. Patterson, X. J. Meng, and P. G. Halbur, Porcine circovirus type 2 in muscle and bone marrow is infectious and transmissible to na??ve pigs by oral consumption, Veterinary Microbiology, vol.133, issue.1-2, pp.54-64, 2009.
DOI : 10.1016/j.vetmic.2008.06.018

K. V. Phenix, J. H. Weston, I. Ypelaar, A. Lavazza, J. A. Smyth et al., Nucleotide sequence analysis of a novel circovirus of canaries and its relationship to other members of the genus Circovirus of the family Circoviridae, Journal of General Virology, vol.82, issue.11, pp.2805-2809, 2001.
DOI : 10.1099/0022-1317-82-11-2805

S. Ramamoorthy and X. J. Meng, Porcine circoviruses: a minuscule yet mammoth paradox, Animal Health Research Reviews, vol.10, issue.01, pp.1-20, 2009.
DOI : 10.1128/CDLI.12.11.1347-1351.2005

K. Rosario, S. Duffy, and M. Breitbart, Diverse circovirus-like genome architectures revealed by environmental metagenomics, Journal of General Virology, vol.90, issue.10, pp.2418-2424, 2009.
DOI : 10.1099/vir.0.012955-0

M. E. Stewart, R. Perry, and S. R. , ) with feather disease, Avian Pathology, vol.108, issue.2, pp.86-92, 2006.
DOI : 10.1016/S0378-1135(99)00070-X

I. Tischer, L. Bode, J. Apodaca, H. Timm, D. Peters et al., Presence of antibodies reacting with porcine circovirus in sera of humans, mice, and cattle, Archives of Virology, vol.140, issue.8, pp.1427-1439, 1995.
DOI : 10.1007/BF01322669

D. Todd, A. N. Scott, E. Fringuelli, H. L. Shivraprasad, D. Gavier-widen et al., Molecular characterization of novel circoviruses from finch and gull, Avian Pathology, vol.71, issue.1, pp.75-81, 2007.
DOI : 10.1177/104063879300500417

D. Todd, J. H. Weston, D. Soike, and J. A. Smyth, Genome Sequence Determinations and Analyses of Novel Circoviruses from Goose and Pigeon, Virology, vol.286, issue.2, pp.354-362, 2001.
DOI : 10.1006/viro.2001.0985

J. G. Victoria, A. Kapoor, L. Li, O. Blinkova, B. Slikas et al., Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis, Journal of Virology, vol.83, issue.9, pp.4642-4651, 2009.
DOI : 10.1128/JVI.02301-08

T. Zhang, M. Breitbart, W. H. Lee, J. Q. Run, C. L. Wei et al., RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses, PLoS Biology, vol.33, issue.1, p.3, 2006.
DOI : 10.1371/journal.pbio.0040003.t005

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, pp.3406-3415, 2003.
DOI : 10.1093/nar/gkg595
URL : http://doi.org/10.1093/nar/gkg595