T. Jartti, L. Jartti, O. Ruuskanen, and M. Söderlund-venermo, New respiratory viral infections, Current Opinion in Pulmonary Medicine, vol.18, issue.3, pp.271-278, 2012.
DOI : 10.1097/MCP.0b013e328351f8d4

. Qu, est-ce que la pneumonie ? -ameli-santé

M. C. Williams, Alveolar Type I Cells: Molecular Phenotype and Development, Annual Review of Physiology, vol.65, issue.1, pp.669-695, 2003.
DOI : 10.1146/annurev.physiol.65.092101.142446

H. Fehrenbach, Alveolar epithelial type II cell: defender of the alveolus revisited, Respiratory Research, vol.2, issue.1, p.33, 2001.
DOI : 10.1186/rr36

L. Sherwood, Physiologie humaine: A Human Perspective, 2006.

M. Vareille, E. Kieninger, M. R. Edwards, and N. Regamey, The Airway Epithelium: Soldier in the Fight against Respiratory Viruses, Clinical Microbiology Reviews, vol.24, issue.1, pp.210-229, 2011.
DOI : 10.1128/CMR.00014-10

C. Coraux, R. Hajj, P. Lesimple, and E. Puchelle, Réparation et régénération de l'épithélium respiratoire, M/S : médecine sciences 21, pp.1063-1069, 2005.

T. J. Nevalainen, G. G. Graham, and K. F. Scott, Antibacterial actions of secreted phospholipases A2. Review, Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, vol.1781, issue.1-2, pp.1-9, 2008.
DOI : 10.1016/j.bbalip.2007.12.001

N. A. Eisele and D. M. Anderson, Host Defense and the Airway Epithelium: Frontline Responses That Protect against Bacterial Invasion and Pneumonia, Journal of Pathogens, vol.160, issue.3, pp.1-16, 2011.
DOI : 10.1023/B:APPT.0000031448.64969.fa

S. B. Gordon and R. C. Read, Macrophage defences against respiratory tract infections, British Medical Bulletin, vol.61, issue.1, pp.45-61, 2002.
DOI : 10.1093/bmb/61.1.45
URL : http://bmb.oxfordjournals.org/cgi/content/short/61/1/45

G. A. Rossi, Human Ciliated Bronchial Epithelial Cells: Expression of the HLA-DR Antigens and of the HLA-DR Alpha Gene, Modulation of the HLA-DR Antigens by Gamma-Interferon and Antigen-presenting Function in the Mixed Leukocyte Reaction, American Journal of Respiratory Cell and Molecular Biology, vol.3, issue.5, pp.431-439, 1990.
DOI : 10.1165/ajrcmb/3.5.431

R. Medzhitov, Toll-like receptors and innate immunity, Nature Reviews Immunology, vol.274, issue.2, pp.135-145, 2001.
DOI : 10.1038/35100529

F. Martinon and J. Tschopp, NLRs join TLRs as innate sensors of pathogens, Trends in Immunology, vol.26, issue.8, pp.447-454, 2005.
DOI : 10.1016/j.it.2005.06.004

Y. Loo and M. G. Jr, Immune Signaling by RIG-I-like Receptors, Immunity, vol.34, issue.5, pp.680-692, 2011.
DOI : 10.1016/j.immuni.2011.05.003

C. Basset, J. Holton, R. O-'mahony, and I. Roitt, Innate immunity and pathogen???host interaction, Vaccine, vol.21, issue.2, pp.12-23, 2003.
DOI : 10.1016/S0264-410X(03)00195-6

R. Bals and P. S. Hiemstra, Innate immunity in the lung: how epithelial cells fight against respiratory pathogens, European Respiratory Journal, vol.23, issue.2, pp.327-333, 2004.
DOI : 10.1183/09031936.03.00098803

W. K. Born, C. L. Reardon, and R. L. O-'brien, The function of ???? T cells in innate immunity, Current Opinion in Immunology, vol.18, issue.1, pp.31-38, 2006.
DOI : 10.1016/j.coi.2005.11.007

V. Brinkmann, Neutrophil Extracellular Traps Kill Bacteria, Science, vol.303, issue.5663, pp.1532-1535, 2004.
DOI : 10.1126/science.1092385

A. Aderem and D. M. Underhill, MECHANISMS OF PHAGOCYTOSIS IN MACROPHAGES, Annual Review of Immunology, vol.17, issue.1, pp.593-623, 1999.
DOI : 10.1146/annurev.immunol.17.1.593

P. Blanco, A. K. Palucka, V. Pascual, and J. Banchereau, Dendritic cells and cytokines in human inflammatory and autoimmune diseases, Cytokine & Growth Factor Reviews, vol.19, issue.1, pp.41-52, 2008.
DOI : 10.1016/j.cytogfr.2007.10.004
URL : https://hal.archives-ouvertes.fr/hal-00275657

E. Vivier, Innate or Adaptive Immunity? The Example of Natural Killer Cells, Science, vol.331, issue.6013, pp.44-49, 2011.
DOI : 10.1126/science.1198687
URL : https://hal.archives-ouvertes.fr/hal-00611585

E. Vivier and N. Anfossi, Inhibitory NK-cell receptors on T cells: witness of the past, actors of the future, Nature Reviews Immunology, vol.170, issue.3, pp.190-198, 2004.
DOI : 10.1038/nri1306

F. Martin and J. F. Kearney, B1 cells: similarities and differences with other B cell subsets, Current Opinion in Immunology, vol.13, issue.2, pp.195-201, 2001.
DOI : 10.1016/S0952-7915(00)00204-1

H. Rus, C. Cudrici, and F. Niculescu, The Role of the Complement System in Innate Immunity, Immunologic Research, vol.33, issue.2, pp.103-112, 2005.
DOI : 10.1385/IR:33:2:103

C. T. Weaver, L. E. Harrington, P. R. Mangan, M. Gavrieli, and K. M. Murphy, Th17: An Effector CD4 T Cell Lineage with Regulatory T Cell Ties, Th17: An Effector CD4 T Cell Lineage with Regulatory T Cell Ties, pp.677-688, 2006.
DOI : 10.1016/j.immuni.2006.06.002

J. J. Shea, Jaks, STATs, Cytokine Signal Transduction, and Immunoregulation: Are We There Yet?, Immunity, vol.7, issue.1, pp.1-11, 1997.
DOI : 10.1016/S1074-7613(00)80505-1

J. J. O-'shea and W. E. Paul, Mechanisms Underlying Lineage Commitment and Plasticity of Helper CD4+ T Cells, Science, vol.327, issue.5969, pp.1098-1102, 2010.
DOI : 10.1126/science.1178334

K. Schwartz, Inflammation & maladies inflammatoires, clés de compréhension (2011) (available at http://www.inserm.fr/associations-de-malades/actualites/inflammation-maladies-inflammatoires-cles-de- comprehension)

B. Min and W. E. Paul, Basophils and type 2 immunity, Current Opinion in Hematology, vol.15, issue.1, pp.59-63, 2008.
DOI : 10.1097/MOH.0b013e3282f13ce8
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403736

S. P. Hogan, Eosinophils: Biological Properties and Role in Health and Disease, Clinical & Experimental Allergy, vol.11, issue.4, pp.709-750, 2008.
DOI : 10.1067/mai.2003.139

S. J. Galli, M. Grimbaldeston, and M. Tsai, Immunomodulatory mast cells: negative, as well as positive, regulators of immunity, Nature Reviews Immunology, vol.35, issue.6, pp.478-486, 2008.
DOI : 10.1038/nri2327

P. J. Barnes, Immunology of asthma and chronic obstructive pulmonary disease, Nature Reviews Immunology, vol.533, issue.3, pp.183-192, 2008.
DOI : 10.1038/nri2254

D. J. Mckeon, Prolonged survival of neutrophils from patients with ??F508 CFTR mutations, Thorax, vol.63, issue.7, pp.660-661, 2008.
DOI : 10.1136/thx.2008.096834

A. Papi, Infections and Airway Inflammation in Chronic Obstructive Pulmonary Disease Severe Exacerbations, American Journal of Respiratory and Critical Care Medicine, vol.173, issue.10, pp.1114-1121, 2006.
DOI : 10.1164/rccm.200506-859OC

I. Rudan, C. Boschi-pinto, Z. Biloglav, K. Mulholland, and H. Campbell, Epidemiology and etiology of childhood pneumonia, Bulletin of the World Health Organization, vol.86, issue.5, pp.408-416, 2008.
DOI : 10.2471/BLT.07.048769

B. Greenwood, A global action plan for the prevention and control of pneumonia, Bulletin of the World Health Organization, vol.86, issue.5, pp.322-322, 2008.
DOI : 10.2471/BLT.08.053348

A. T. Pavia, Viral Infections of the Lower Respiratory Tract: Old Viruses, New Viruses, and the Role of Diagnosis, Clinical Infectious Diseases, vol.52, issue.Supplement 4, pp.284-289, 2011.
DOI : 10.1093/cid/cir043

F. Blasi, Atypical pathogens and respiratory tract infections, European Respiratory Journal, vol.24, issue.1, pp.171-182, 2004.
DOI : 10.1183/09031936.04.00135703

T. Marrie, The Role of Atypical Pathogens in Community-Acquired Pneumonia, Seminars in Respiratory and Critical Care Medicine 33, pp.244-256, 2012.

C. Hyams, Streptococcus pneumoniae Resistance to Complement-Mediated Immunity Is Dependent on the Capsular Serotype, Infection and Immunity, vol.78, issue.2, pp.716-725, 2010.
DOI : 10.1128/IAI.01056-09

A. Martner, C. Dahlgren, J. C. Paton, and A. E. Wold, Pneumolysin Released during Streptococcus pneumoniae Autolysis Is a Potent Activator of Intracellular Oxygen Radical Production in Neutrophils, Infection and Immunity, vol.76, issue.9, pp.4079-4087, 2008.
DOI : 10.1128/IAI.01747-07

A. Kadioglu, J. N. Weiser, J. C. Paton, and P. W. Andrew, The role of Streptococcus pneumoniae virulence factors in host respiratory colonization and disease, Nature Reviews Microbiology, vol.74, issue.4, pp.288-301, 2008.
DOI : 10.1038/nrmicro1871

W. P. Hausdorff and R. Dagan, Serotypes and pathogens in paediatric pneumonia, Vaccine, vol.26, issue.2, pp.19-23, 2008.
DOI : 10.1016/j.vaccine.2008.05.033

A. L. Erwin and A. L. Smith, Nontypeable Haemophilus influenzae: understanding virulence and commensal behavior, Trends in Microbiology, vol.15, issue.8, pp.355-362, 2007.
DOI : 10.1016/j.tim.2007.06.004

E. S. Lysenko, A. J. Ratner, A. L. Nelson, and J. N. Weiser, The Role of Innate Immune Responses in the Outcome of Interspecies Competition for Colonization of Mucosal Surfaces, PLoS Pathogens, vol.261, issue.1, 2005.
DOI : 0193-4511(1993)261[0358:MOUROB]2.0.CO;2

S. D. Haessler and R. B. Brown, Pneumonia Caused by Staphylococcus aureus, Current Respiratory Medicine Reviews, vol.5, issue.1, pp.62-67, 2009.
DOI : 10.2174/157339809787354056

I. Puljiz, I. Kuzman, O. Dakovic-rode, N. Schönwald, and B. Mise, Chlamydia pneumoniae and Mycoplasma pneumoniae pneumonia: comparison of clinical, epidemiological characteristics and laboratory profiles, Epidemiology and Infection, vol.134, issue.03, pp.548-555, 2006.
DOI : 10.1017/S0950268805005522

M. Woodhead, Community-acquired pneumonia in Europe: causative pathogens and resistance patterns, European Respiratory Journal, vol.20, issue.Supplement 36, pp.20-27, 2002.
DOI : 10.1183/09031936.02.00702002

A. M. Kesson, Respiratory virus infections, Paediatric Respiratory Reviews, vol.8, issue.3, pp.240-248, 2007.
DOI : 10.1016/j.prrv.2007.07.003

M. Korppi, M. Don, F. Valent, and M. Canciani, The value of clinical features in differentiating between viral, pneumococcal and atypical bacterial pneumonia in children, Acta Paediatrica, vol.29, issue.7, pp.943-947, 2008.
DOI : 10.1086/338460

W. J. Barson, Clinical features and diagnosis of community-acquired pneumonia in children (2012) (available at http://www.uptodate.com/contents/clinical-features-and-diagnosis-of-community-acquired-pneumonia-in-children)

W. F. Carman and J. B. Mahony, The pathogens, Journal of Clinical Virology, vol.40, pp.5-10, 2007.
DOI : 10.1016/S1386-6532(07)70003-3

O. Ruuskanen, E. Lahti, L. C. Jennings, and D. R. Murdoch, Viral pneumonia, The Lancet, vol.377, issue.9773, pp.1264-1275, 2011.
DOI : 10.1016/S0140-6736(10)61459-6

W. M. Sullender, Respiratory Syncytial Virus Genetic and Antigenic Diversity, Clinical Microbiology Reviews, vol.13, issue.1, pp.1-15, 2000.
DOI : 10.1128/CMR.13.1.1-15.2000
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC88930

W. P. Glezen, A. L. Frank, L. H. Taber, and J. A. , Parainfluenza Virus Type 3: Seasonality and Risk of Infection and Reinfection in Young Children, Journal of Infectious Diseases, vol.150, issue.6, pp.851-857, 1984.
DOI : 10.1093/infdis/150.6.851

W. Kunze, D. Beier, and K. Groeger, Adenovirus Respiratory Infections In Children. Do They Mimic Bacterial Infections?, 2010.

J. P. Lynch-3rd, M. Fishbein, and M. Echavarria, Adenovirus, Seminars in Respiratory and Critical Care Medicine, vol.32, issue.04, pp.494-511, 2011.
DOI : 10.1055/s-0031-1283287

W. Lee, A Diverse Group of Previously Unrecognized Human Rhinoviruses Are Common Causes of Respiratory Illnesses in Infants, PLoS ONE, vol.38, issue.1, p.966, 2007.
DOI : 10.1371/journal.pone.0000966.t004

S. B. Greenberg, Respiratory Consequences of Rhinovirus Infection, Archives of Internal Medicine, vol.163, issue.3, pp.278-284, 2003.
DOI : 10.1001/archinte.163.3.278

M. Debiaggi, F. Canducci, E. R. Ceresola, and M. Clementi, The role of infections and coinfections with newly identified and emerging respiratory viruses in children, Virology Journal, vol.9, issue.1, p.247, 2012.
DOI : 10.1097/INF.0b013e318162a14f

M. G. Sy and J. L. Robinson, Community-acquired Moraxella catarrhalis pneumonia in previously healthy children, Pediatric Pulmonology, vol.80, issue.7, pp.674-678, 2010.
DOI : 10.1002/ppul.21243

G. Cortés, D. Álvarez, C. Saus, and S. Albertí, Role of Lung Epithelial Cells in Defense against Klebsiella pneumoniae Pneumonia, Infection and Immunity, vol.70, issue.3, pp.1075-1080, 2002.
DOI : 10.1128/IAI.70.3.1075-1080.2002

K. A. Beynon, in Adult Pneumonia Patients1, Emerging Infectious Diseases, vol.11, issue.4, pp.639-641, 2005.
DOI : 10.3201/eid1104.040822

J. S. Kahn, Epidemiology of Human Metapneumovirus, Clinical Microbiology Reviews, vol.19, issue.3, pp.546-557, 2006.
DOI : 10.1128/CMR.00014-06

J. V. Williams, Human Metapneumovirus and Lower Respiratory Tract Disease in Otherwise Healthy Infants and Children, New England Journal of Medicine, vol.350, issue.5, pp.443-450, 2004.
DOI : 10.1056/NEJMoa025472

C. Manoha, S. Espinosa, S. Aho, F. Huet, and P. Pothier, Epidemiological and clinical features of hMPV, RSV and RVs infections in young children, Journal of Clinical Virology, vol.38, issue.3, pp.221-226, 2007.
DOI : 10.1016/j.jcv.2006.12.005
URL : https://hal.archives-ouvertes.fr/hal-00465382

A. Manning, Epidemiological Profile and Clinical Associations of Human Bocavirus and Other Human Parvoviruses, The Journal of Infectious Diseases, vol.194, issue.9, pp.1283-1290, 2006.
DOI : 10.1086/508219

O. Schildgen, Human Bocavirus: Passenger or Pathogen in Acute Respiratory Tract Infections?, Clinical Microbiology Reviews, vol.21, issue.2, pp.291-304, 2008.
DOI : 10.1128/CMR.00030-07

P. Berche, Faut-il encore avoir peur de la grippe ? : Histoire des pandémies, 2012.

J. Kuypers, Clinical Disease in Children Associated With Newly Described Coronavirus Subtypes, PEDIATRICS, vol.119, issue.1, pp.70-76, 2007.
DOI : 10.1542/peds.2006-1406

Y. Abed and G. Boivin, Molecular Characterization of Viruses from Clinical Respiratory Samples Producing Unidentified Cytopathic Effects in Cell Culture, Viruses, vol.1, issue.2, pp.84-90, 2009.
DOI : 10.3390/v1020084

Z. Xiang, Coxsackievirus A21, Enterovirus 68, and Acute Respiratory Tract Infection, China, Emerging Infectious Diseases, vol.18, issue.5, pp.821-824, 2012.
DOI : 10.3201/eid1805.111376
URL : https://hal.archives-ouvertes.fr/hal-00965853

A. Piralla, Clinical severity and molecular typing of human rhinovirus C strains during a fall outbreak affecting hospitalized patients, Journal of Clinical Virology, vol.45, issue.4, pp.311-317, 2009.
DOI : 10.1016/j.jcv.2009.04.016

V. Foulongne, KI and WU Polyomaviruses in Children, France, Emerging Infectious Diseases, vol.14, issue.3, pp.523-525, 2008.
DOI : 10.3201/eid1403.071206

R. Gonzales, D. C. Malone, J. H. Maselli, and M. A. Sande, Excessive Antibiotic Use for Acute Respiratory Infections in the United States, Clinical Infectious Diseases, vol.33, issue.6, pp.757-762, 2001.
DOI : 10.1086/322627

J. S. Tregoning and J. Schwarze, Respiratory Viral Infections in Infants: Causes, Clinical Symptoms, Virology, and Immunology, Clinical Microbiology Reviews, vol.23, issue.1, pp.74-98, 2010.
DOI : 10.1128/CMR.00032-09

W. A. Knaus, E. A. Draper, D. P. Wagner, and J. E. Zimmerman, APACHE II, Critical Care Medicine, vol.13, issue.10, pp.818-829, 1985.
DOI : 10.1097/00003246-198510000-00009

W. S. Lim, Defining community acquired pneumonia severity on presentation to hospital: an international derivation and validation study, Thorax, vol.58, issue.5, pp.377-382, 2003.
DOI : 10.1136/thorax.58.5.377

R. Seligman, Biomarkers in community-acquired pneumonia: A state-of-the-art review, Clinics, vol.67, issue.11, pp.1321-1325, 2012.
DOI : 10.6061/clinics/2012(11)17

J. Hedlund and L. O. Hansson, Procalcitonin and C-Reactive Protein Levels in Community-Acquired Pneumonia: Correlation with Etiology and Prognosis, Infection, vol.28, issue.2, pp.68-73, 2000.
DOI : 10.1007/s150100050049

M. Falguera, Predictive factors, microbiology and outcome of patients with parapneumonic effusion, European Respiratory Journal, vol.38, issue.5, pp.1173-1179, 2011.
DOI : 10.1183/09031936.00000211

A. Girdhar, A. Shujaat, and A. Bajwa, Management of Infectious Processes of the Pleural Space: A Review, Pulmonary Medicine, vol.105, issue.3, p.816502, 2012.
DOI : 10.1016/0003-4975(96)00194-4

D. S. Leland and C. C. Ginocchio, Role of Cell Culture for Virus Detection in the Age of Technology, Clinical Microbiology Reviews, vol.20, issue.1, pp.49-78, 2007.
DOI : 10.1128/CMR.00002-06

M. Ogilvie, Molecular techniques shouldnot now replace cell culture in diagnostic virology laboratories, Reviews in Medical Virology, vol.53, issue.6, pp.351-354, 2001.
DOI : 10.1002/rmv.335

P. Roingeard, Viral detection by electron microscopy: past, present and future, Biology of the Cell, vol.312, issue.8, pp.491-501, 2008.
DOI : 10.1042/BC20070173
URL : https://hal.archives-ouvertes.fr/inserm-00308276

W. K. Aldous, A comparison of binax??? now?? to viral culture and direct fluorescent assay testing for respiratory syncytial virus, Diagnostic Microbiology and Infectious Disease, vol.49, issue.4, pp.265-268, 2004.
DOI : 10.1016/j.diagmicrobio.2004.04.005

M. L. Landry, S. Cohen, and D. Ferguson, Comparison of Binax NOW and Directigen for rapid detection of influenza A and B, Journal of Clinical Virology, vol.31, issue.2, pp.113-115, 2004.
DOI : 10.1016/j.jcv.2004.04.005

S. F. Dowell, R. L. Garman, G. Liu, O. S. Levine, and Y. Yang, Evaluation of Binax NOW, an Assay for the Detection of Pneumococcal Antigen in Urine Samples, Performed among Pediatric Patients, Clinical Infectious Diseases, vol.32, issue.5, pp.824-825, 2001.
DOI : 10.1086/319205

J. B. Mahony, Detection of Respiratory Viruses by Molecular Methods, Clinical Microbiology Reviews, vol.21, issue.4, pp.716-747, 2008.
DOI : 10.1128/CMR.00037-07

J. D. Fox, Nucleic acid amplification tests for detection of respiratory viruses, Journal of Clinical Virology, vol.40, pp.15-23, 2007.
DOI : 10.1016/S1386-6532(07)70005-7

M. Ieven, Currently used nucleic acid amplification tests for the detection of viruses and atypicals in acute respiratory infections, Journal of Clinical Virology, vol.40, issue.4, pp.259-276, 2007.
DOI : 10.1016/j.jcv.2007.08.012

T. Hyypiä, Detection of adenovirus in nasopharyngeal specimens by radioactive and nonradioactive DNA probes, J Clin Microbiol, vol.21, pp.730-733, 1985.

K. Pabbaraju, K. L. Tokaryk, S. Wong, and J. D. Fox, Comparison of the Luminex xTAG Respiratory Viral Panel with In-House Nucleic Acid Amplification Tests for Diagnosis of Respiratory Virus Infections, Journal of Clinical Microbiology, vol.46, issue.9, pp.3056-3062, 2008.
DOI : 10.1128/JCM.00878-08

B. Lin, Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays, Genome Research, vol.16, issue.4, pp.527-535, 2006.
DOI : 10.1101/gr.4337206

S. R. Dominguez, Multiplex MassTag-PCR for respiratory pathogens in pediatric nasopharyngeal washes negative by conventional diagnostic testing shows a high prevalence of viruses belonging to a newly recognized rhinovirus clade, Journal of Clinical Virology, vol.43, issue.2, pp.219-222, 2008.
DOI : 10.1016/j.jcv.2008.06.007

D. R. Murdoch, Laboratory Methods for Determining Pneumonia Etiology in Children, Clinical Infectious Diseases, vol.54, issue.suppl 2, pp.146-152, 2012.
DOI : 10.1093/cid/cir1073

T. Nishizawa, A Novel DNA Virus (TTV) Associated with Elevated Transaminase Levels in Posttransfusion Hepatitis of Unknown Etiology, Biochemical and Biophysical Research Communications, vol.241, issue.1, pp.92-97, 1997.
DOI : 10.1006/bbrc.1997.7765

A. S. Muerhoff, T. P. Leary, S. M. Desai, and I. K. Mushahwar, Amplification and subtraction methods and their application to the discovery of novel human viruses, Journal of Medical Virology, vol.222, issue.1, pp.96-103, 1997.
DOI : 10.1002/(SICI)1096-9071(199709)53:1<96::AID-JMV16>3.0.CO;2-V

H. E. Ambrose and J. P. Clewley, Virus discovery by sequence-independent genome amplification, Reviews in Medical Virology, vol.266, issue.6, pp.365-383, 2006.
DOI : 10.1002/rmv.515

L. G. Birkenmeyer, Selectively primed adaptive driver RDA (SPAD-RDA): An improved method for subtractive hybridization, Journal of Medical Virology, vol.23, issue.1, pp.150-159, 2003.
DOI : 10.1002/jmv.10460

P. Biagini, X. De-lamballerie, and P. De-micco, Effective detection of highly divergent viral genomes in infected cell lines using a new subtraction strategy (primer extension enrichment reaction???PEER), Journal of Virological Methods, vol.139, issue.1, pp.106-110, 2007.
DOI : 10.1016/j.jviromet.2006.09.010

L. Van-der-hoek, Identification of a new human coronavirus, Nature Medicine, vol.10, issue.4, pp.368-373, 2004.
DOI : 10.1038/nm1024

T. Allander, From The Cover: Cloning of a human parvovirus by molecular screening of respiratory tract samples, Proceedings of the National Academy of Sciences, vol.102, issue.36, pp.12891-12896, 2005.
DOI : 10.1073/pnas.0504666102

N. Berthet, Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR, BMC Molecular Biology, vol.9, issue.1, p.77, 2008.
DOI : 10.1186/1471-2199-9-77

P. Biagini, Circular genomes related to anelloviruses identified in human and animal samples by using a combined rolling-circle amplification/sequence-independent single primer amplification approach, Journal of General Virology, vol.88, issue.10, pp.2696-2701, 2007.
DOI : 10.1099/vir.0.83071-0
URL : https://hal.archives-ouvertes.fr/hal-01076924

R. Johne, H. Müller, A. Rector, M. Van-ranst, and H. Stevens, Rolling-circle amplification of viral DNA genomes using phi29 polymerase, Trends in Microbiology, vol.17, issue.5, pp.205-211, 2009.
DOI : 10.1016/j.tim.2009.02.004

M. L. Metzker, Sequencing technologies ??? the next generation, Nature Reviews Genetics, vol.37, issue.1, pp.31-46, 2010.
DOI : 10.1038/nrg2626

K. V. Voelkerding, S. Dames, and J. D. Durtschi, Next Generation Sequencing for Clinical Diagnostics-Principles and Application to Targeted Resequencing for Hypertrophic Cardiomyopathy, The Journal of Molecular Diagnostics, vol.12, issue.5, pp.539-551, 2010.
DOI : 10.2353/jmoldx.2010.100043

R. Blervaque, Biorigami -Site francophone de biotechnologies, 2011.

L. Barzon, E. Lavezzo, V. Militello, S. Toppo, and G. Palù, Applications of Next-Generation Sequencing Technologies to Diagnostic Virology, International Journal of Molecular Sciences, vol.12, issue.12, pp.7861-7884, 2011.
DOI : 10.3390/ijms12117861

J. Yang, Unbiased Parallel Detection of Viral Pathogens in Clinical Samples by Use of a Metagenomic Approach, Journal of Clinical Microbiology, vol.49, issue.10, pp.3463-3469, 2011.
DOI : 10.1128/JCM.00273-11

F. Lysholm, Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing, PLoS ONE, vol.78, issue.2, p.30875, 2012.
DOI : 10.1371/journal.pone.0030875.s006

S. Bousbia, Repertoire of Intensive Care Unit Pneumonia Microbiota, PLoS ONE, vol.73, issue.2, p.32486, 2012.
DOI : 10.1371/journal.pone.0032486.s021

C. U. Köser, Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak, New England Journal of Medicine, vol.366, issue.24, pp.2267-2275, 2012.
DOI : 10.1056/NEJMoa1109910

W. I. Lipkin and P. Discovery, Pathogen Discovery, PLoS Pathogens, vol.250, issue.7, p.1000002, 2008.
DOI : 10.1371/journal.ppat.1000002.g001

A. Thomson and M. Harris, Community-acquired pneumonia in children: what's new?, Thorax, vol.66, issue.10, pp.927-928, 2011.
DOI : 10.1136/thoraxjnl-2011-200671

P. Biagini, Anelloviridae -Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses, 2011.

H. Okamoto, History of Discoveries and Pathogenicity of TT Viruses, Curr. Top. Microbiol. Immunol, vol.331, pp.1-20, 2009.
DOI : 10.1007/978-3-540-70972-5_1

Y. Itoh, Visualization of TT Virus Particles Recovered from the Sera and Feces of Infected Humans, Biochemical and Biophysical Research Communications, vol.279, issue.2, pp.718-724, 2000.
DOI : 10.1006/bbrc.2000.4013

H. Okamoto, Molecular cloning and characterization of a novel DNA virus (TTV) associated with posttransfusion hepatitis of unknown etiology, Hepatology Research, vol.10, issue.1, pp.1-16, 1998.
DOI : 10.1016/S1386-6346(97)00123-X

I. K. Mushahwar, Molecular and biophysical characterization of TT virus: Evidence for a new virus family infecting humans, Proceedings of the National Academy of Sciences, vol.96, issue.6, pp.3177-3182, 1999.
DOI : 10.1073/pnas.96.6.3177

P. Biagini, Classification of TTV and Related Viruses (Anelloviruses), Curr. Top. Microbiol. Immunol, vol.331, pp.21-33, 2009.
DOI : 10.1007/978-3-540-70972-5_2
URL : https://hal.archives-ouvertes.fr/halshs-00637837

K. Takahashi, Y. Iwasa, M. Hijikata, and S. Mishiro, Identification of a new human DNA virus (TTV-like mini virus, TLMV) intermediately related to TT virus and chicken anemia virus, Archives of Virology, vol.145, issue.5, pp.979-993, 2000.
DOI : 10.1007/s007050050689

M. Ninomiya, Identification and genomic characterization of a novel human torque teno virus of 3.2 kb, Journal of General Virology, vol.88, issue.7, pp.1939-1944, 2007.
DOI : 10.1099/vir.0.82895-0

M. S. Jones, New DNA Viruses Identified in Patients with Acute Viral Infection Syndrome, Journal of Virology, vol.79, issue.13, pp.8230-8236, 2005.
DOI : 10.1128/JVI.79.13.8230-8236.2005

H. Okamoto, TT Viruses in Animals, Curr. Top. Microbiol. Immunol, vol.331, pp.35-52, 2009.
DOI : 10.1007/978-3-540-70972-5_3

T. F. Ng, W. K. Suedmeyer, E. Wheeler, F. Gulland, and M. Breitbart, Novel anellovirus discovered from a mortality event of captive California sea lions, Journal of General Virology, vol.90, issue.5, pp.1256-1261, 2009.
DOI : 10.1099/vir.0.008987-0

T. Kekarainen and J. Segalés, Torque teno virus infection in the pig and its potential role as a model of human infection, The Veterinary Journal, vol.180, issue.2, pp.163-168, 2009.
DOI : 10.1016/j.tvjl.2007.12.005

F. Maggi and M. Bendinelli, Human anelloviruses and the central nervous system, Reviews in Medical Virology, vol.12, issue.6, pp.392-407, 2010.
DOI : 10.1002/rmv.668

P. Biagini and P. De-micco, La famille des Anelloviridae : virus TTV et genres apparentés, Virologie, vol.14, pp.3-16, 2010.

I. Davidson and L. M. Shulman, Unraveling the puzzle of human anellovirus infections by comparison with avian infections with the chicken anemia virus, Virus Research, vol.137, issue.1, pp.1-15, 2008.
DOI : 10.1016/j.virusres.2008.06.014

S. Hino and A. A. Prasetyo, Relationship of Torque Teno Virus to Chicken Anemia Virus, Curr. Top. Microbiol. Immunol, vol.331, pp.117-130, 2009.
DOI : 10.1007/978-3-540-70972-5_8

M. Bendinelli, Molecular Properties, Biology, and Clinical Implications of TT Virus, a Recently Identified Widespread Infectious Agent of Humans, Clinical Microbiology Reviews, vol.14, issue.1, pp.98-113, 2001.
DOI : 10.1128/CMR.14.1.98-113.2001

T. Kamahora, S. Hino, and H. Miyata, Three Spliced mRNAs of TT Virus Transcribed from a Plasmid Containing the Entire Genome in COS1 Cells, Journal of Virology, vol.74, issue.21, pp.9980-9986, 2000.
DOI : 10.1128/JVI.74.21.9980-9986.2000

J. Qiu, Human Circovirus TT Virus Genotype 6 Expresses Six Proteins following Transfection of a Full-Length Clone, Journal of Virology, vol.79, issue.10, pp.6505-6510, 2005.
DOI : 10.1128/JVI.79.10.6505-6510.2005

L. Leppik, In Vivo and In Vitro Intragenomic Rearrangement of TT Viruses, Journal of Virology, vol.81, issue.17, pp.9346-9356, 2007.
DOI : 10.1128/JVI.00781-07

T. Suzuki, Identification of Basal Promoter and Enhancer Elements in an Untranslated Region of the TT Virus Genome, Journal of Virology, vol.78, issue.19, pp.10820-10824, 2004.
DOI : 10.1128/JVI.78.19.10820-10824.2004

K. Kamada, T. Kamahora, P. Kabat, and S. Hino, Transcriptional regulation of TT virus: promoter and enhancer regions in the 1.2-kb noncoding region, Virology, vol.321, issue.2, pp.341-348, 2004.
DOI : 10.1016/j.virol.2003.12.024

L. Kakkola, Expression of all six human Torque teno virus (TTV) proteins in bacteria and in insect cells, and analysis of their IgG responses, Virology, vol.382, issue.2, pp.182-189, 2008.
DOI : 10.1016/j.virol.2008.09.012

L. Kakkola, K. Hedman, J. Qiu, D. Pintel, and M. , Söderlund-Venermo, Replication of and protein synthesis by TT viruses, Curr. Top. Microbiol. Immunol, vol.331, pp.53-64, 2009.

H. Okamoto, The 5'-terminal sequence of the hepatitis C virus genome, Jpn. J. Exp. Med, vol.60, pp.167-177, 1990.

T. Pollicino, TT virus has a ubiquitous diffusion in human body tissues: analyses of paired serum and tissue samples, Journal of Viral Hepatitis, vol.73, issue.2, pp.95-102, 2003.
DOI : 10.1002/jmv.2051

J. C. Erker, T. P. Leary, S. M. Desai, M. L. Chalmers, and I. K. Mushahwar, Analyses of TT virus full-length genomic sequences., Journal of General Virology, vol.80, issue.7, pp.1743-1750, 1999.
DOI : 10.1099/0022-1317-80-7-1743

H. Zheng, Torque Teno Virus (SANBAN Isolate) ORF2 Protein Suppresses NF-??B Pathways via Interaction with I??B Kinases, Journal of Virology, vol.81, issue.21, pp.11917-11924, 2007.
DOI : 10.1128/JVI.01101-07

M. A. Peters, D. C. Jackson, B. S. Crabb, and G. F. Browning, Chicken Anemia Virus VP2 Is a Novel Dual Specificity Protein Phosphatase, Journal of Biological Chemistry, vol.277, issue.42, pp.39566-39573, 2002.
DOI : 10.1074/jbc.M201752200

S. Asabe, T. Nishizawa, H. Iwanari, and H. Okamoto, Phosphorylation of Serine-Rich Protein Encoded by Open Reading Frame 3 of the TT Virus Genome, Biochemical and Biophysical Research Communications, vol.286, issue.2, pp.298-304, 2001.
DOI : 10.1006/bbrc.2001.5385

B. Mueller, A. Maerz, K. Doberstein, T. Finsterbusch, and A. Mankertz, Gene expression of the human Torque Teno Virus isolate P/1C1, Virology, vol.381, issue.1, pp.36-45, 2008.
DOI : 10.1016/j.virol.2008.08.017

L. Martínez-guinó, M. Ballester, J. Segalés, and T. Kekarainen, Expression profile and subcellular localization of Torque teno sus virus proteins, Journal of General Virology, vol.92, issue.10, pp.2446-2457, 2011.
DOI : 10.1099/vir.0.033134-0

C. Jinling, Bioinformatics analysis on ORF1 protein of Torque teno virus (SANBAN isolate), Asian Pacific Journal of Tropical Medicine, vol.4, issue.11, pp.850-856, 2011.
DOI : 10.1016/S1995-7645(11)60207-1

F. Maggi, Role of Hematopoietic Cells in the Maintenance of Chronic Human Torquetenovirus Plasma Viremia, Journal of Virology, vol.84, issue.13, pp.6891-6893, 2010.
DOI : 10.1128/JVI.00273-10

Y. Kanda, TT Virus in Bone Marrow Transplant Recipients, Blood, vol.93, pp.2485-2490, 1999.

F. Maggi, Dynamics of Persistent TT Virus Infection, as Determined in Patients Treated with Alpha Interferon for Concomitant Hepatitis C Virus Infection, Journal of Virology, vol.75, issue.24, pp.11999-12004, 2001.
DOI : 10.1128/JVI.75.24.11999-12004.2001

F. Maggi, TT Virus in the Nasal Secretions of Children with Acute Respiratory Diseases: Relations to Viremia and Disease Severity, Journal of Virology, vol.77, issue.4, pp.2418-2425, 2003.
DOI : 10.1128/JVI.77.4.2418-2425.2003

L. Kakkola, Construction and biological activity of a full-length molecular clone of human Torque teno virus (TTV) genotype???6, FEBS Journal, vol.132, issue.18, pp.4719-4730, 2007.
DOI : 10.1111/j.1742-4658.2007.06020.x

B. Grasland, Circovirus et pathologies associées chez les animaux, Virologie, vol.9, pp.431-442, 2005.

E. De-villiers, S. S. Borkosky, R. Kimmel, K. Gunst, and J. Fei, The Diversity of Torque Teno Viruses: In Vitro Replication Leads to the Formation of Additional Replication-Competent Subviral Molecules, Journal of Virology, vol.85, issue.14, pp.7284-7295, 2011.
DOI : 10.1128/JVI.02472-10

F. Faurez, D. Dory, B. Grasland, and A. Jestin, Replication of porcine circoviruses, Virology Journal, vol.6, issue.1, p.60, 2009.
DOI : 10.1186/1743-422X-6-60
URL : https://hal.archives-ouvertes.fr/hal-00404743

S. S. Borkosky, C. Whitley, A. Kopp-schneider, H. Zur-hausen, and E. Villiers, Epstein-Barr Virus Stimulates Torque Teno Virus Replication: A Possible Relationship to Multiple Sclerosis, PLoS ONE, vol.3, issue.2, p.32160, 2012.
DOI : 10.1371/journal.pone.0032160.t001

I. Jelcic, A. Hotz-wagenblatt, A. Hunziker, H. Zur-hausen, and E. Villiers, Isolation of Multiple TT Virus Genotypes from Spleen Biopsy Tissue from a Hodgkin's Disease Patient: Genome Reorganization and Diversity in the Hypervariable Region, Journal of Virology, vol.78, issue.14, pp.7498-7507, 2004.
DOI : 10.1128/JVI.78.14.7498-7507.2004

E. M. De-villiers, R. Kimmel, L. Leppik, and K. Gunst, Intragenomic Rearrangement in TT Viruses: A Possible Role in the Pathogenesis of Disease, Curr. Top. Microbiol. Immunol, vol.331, pp.91-107, 2009.
DOI : 10.1007/978-3-540-70972-5_6

M. Ninomiya, M. Takahashi, T. Nishizawa, T. Shimosegawa, and H. Okamoto, Development of PCR Assays with Nested Primers Specific for Differential Detection of Three Human Anelloviruses and Early Acquisition of Dual or Triple Infection during Infancy, Journal of Clinical Microbiology, vol.46, issue.2, pp.507-514, 2008.
DOI : 10.1128/JCM.01703-07

T. Chen, E. Väisänen, P. S. Mattila, K. Hedman, and M. Söderlund-venermo, Antigenic diversity and seroprevalences of Torque teno viruses in children and adults by ORF2-based immunoassays, Journal of General Virology, vol.94, issue.Pt_2, pp.409-417, 2013.
DOI : 10.1099/vir.0.046862-0

P. Biagini and P. De-micco, Les anellovirus (TTV et variants)??: donn??es actuelles dix ans apr??s leur d??couverte, Transfusion Clinique et Biologique, vol.15, issue.6, pp.406-415, 2008.
DOI : 10.1016/j.tracli.2008.10.003

J. K. Ball, TT virus sequence heterogeneity in vivo: evidence for co-infection with multiple genetic types., Journal of General Virology, vol.80, issue.7, pp.1759-1768, 1999.
DOI : 10.1099/0022-1317-80-7-1759

P. Biagini, Determination and phylogenetic analysis of partial sequences from TT virus isolates., Journal of General Virology, vol.80, issue.2, pp.419-424, 1999.
DOI : 10.1099/0022-1317-80-2-419

P. Biagini, Distribution and genetic analysis of TTV and TTMV major phylogenetic groups in French blood donors, Journal of Medical Virology, vol.41, issue.2, pp.298-304, 2006.
DOI : 10.1002/jmv.20539

P. Biagini, P. De-micco, and X. De-lamballerie, Identification of a third member of the Anellovirus genus (???small anellovirus???) in French blood donors, Archives of Virology, vol.145, issue.2, pp.405-408, 2006.
DOI : 10.1007/s00705-005-0660-4

P. Biagini, High prevalence of TT virus infection in French blood donors revealed by the use of three PCR systems, Transfusion, vol.93, issue.5, pp.590-595, 2000.
DOI : 10.1007/s005350050249

J. J. Lefrère, Natural history of the TT virus infection through follow-up of TTV DNA-positive multipletransfused patients, Blood, vol.95, pp.347-351, 2000.

F. Maggi, Relationships between Total Plasma Load of Torquetenovirus (TTV) and TTV Genogroups Carried, Journal of Clinical Microbiology, vol.43, issue.9, pp.4807-4810, 2005.
DOI : 10.1128/JCM.43.9.4807-4810.2005

M. Pistello, TT virus levels in the plasma of infected individuals with different hepatic and extrahepatic pathology, Journal of Medical Virology, vol.11, issue.2, pp.189-195, 2001.
DOI : 10.1002/1096-9071(20000201)63:2<189::AID-JMV1014>3.0.CO;2-H

S. Devalle and C. , Distribution of TT virus genomic groups 1-5 in Brazilian blood donors, HBV carriers, and HIV-1-infected patients, Journal of Medical Virology, vol.74, issue.1, pp.166-173, 2004.
DOI : 10.1002/jmv.10564

S. Hino and H. Miyata, Torque teno virus (TTV): current status, Reviews in Medical Virology, vol.83, issue.1, pp.45-57, 2007.
DOI : 10.1002/rmv.524

S. L. Smits, High Prevalence of Anelloviruses in Vitreous Fluid of Children With Seasonal Hyperacute Panuveitis, Journal of Infectious Diseases, vol.205, issue.12, pp.1877-1884, 2012.
DOI : 10.1093/infdis/jis284

H. Matsubara, Existence of TT Virus DNA in Extracellular Body Fluids from Normal Healthy Japanese Subjects, Intervirology, vol.43, issue.1, pp.16-19, 2000.
DOI : 10.1159/000025018

M. Takahashi, TT Virus Is Distributed in Various Leukocyte Subpopulations at Distinct Levels, with the Highest Viral Load in Granulocytes, Biochemical and Biophysical Research Communications, vol.290, issue.1, pp.242-248, 2002.
DOI : 10.1006/bbrc.2001.6183

F. Maggi, TT virus (TTV) loads associated with different peripheral blood cell types and evidence for TTV replication in activated mononuclear cells, Journal of Medical Virology, vol.59, issue.2, pp.190-194, 2001.
DOI : 10.1002/jmv.1035

E. De-villiers, R. Schmidt, H. Delius, and H. Zur-hausen, Heterogeneity of TT virus related sequences isolated from human tumour biopsy specimens, Journal of Molecular Medicine, vol.80, issue.1, pp.44-50, 2002.
DOI : 10.1007/s001090100281

H. Okamoto, Heterogeneous Distribution of TT Virus of Distinct Genotypes in Multiple Tissues from Infected Humans, Virology, vol.288, issue.2, pp.358-368, 2001.
DOI : 10.1006/viro.2001.1097

A. D. Vecchia, First description of Adenovirus, Enterovirus, Rotavirus and Torque teno virus in water samples collected from the Arroio Dil??vio, Porto Alegre, Brazil, Brazilian Journal of Biology, vol.72, issue.2, pp.323-329, 2012.
DOI : 10.1590/S1519-69842012000200013

K. Chikasue, Detection of Torque teno virus DNA in exhaled breath by polymerase chain reaction, Acta Med. Okayama, vol.66, pp.387-397, 2012.

S. Bédarida, O. Dutour, A. P. Buzhilova, P. De-micco, and P. Biagini, Identification of viral DNA (Anelloviridae) in a 200-year-old dental pulp sample (Napoleon's Great Army, Kaliningrad, 1812), Infection, Genetics and Evolution, vol.11, issue.2, pp.358-362, 2011.
DOI : 10.1016/j.meegid.2010.11.007

M. Pifferi, Associations between Nasal Torquetenovirus Load and Spirometric Indices in Children with Asthma, The Journal of Infectious Diseases, vol.192, issue.7, pp.1141-1148, 2005.
DOI : 10.1086/444389

M. Pifferi, High Torquetenovirus Loads Are Correlated With Bronchiectasis and Peripheral Airflow Limitation in Children, The Pediatric Infectious Disease Journal, vol.25, issue.9, pp.804-808, 2006.
DOI : 10.1097/01.inf.0000232723.58355.f4

F. Maggi, Torquetenovirus in patients with arthritis, Rheumatology, vol.46, issue.5, pp.885-886, 2007.
DOI : 10.1093/rheumatology/kem032

J. Rocchi, Torquetenovirus DNA drives proinflammatory cytokines production and secretion by immune cells via toll-like receptor 9, Virology, vol.394, issue.2, pp.235-242, 2009.
DOI : 10.1016/j.virol.2009.08.036

M. Pifferi, Torquetenovirus Infection and Ciliary Dysmotility in Children With Recurrent Pneumonia, The Pediatric Infectious Disease Journal, vol.27, issue.5, pp.413-418, 2008.
DOI : 10.1097/INF.0b013e318162a14f

F. Maggi, Correlation between Torque Tenovirus Infection and Serum Levels of Eosinophil Cationic Protein in Children Hospitalized for Acute Respiratory Diseases, The Journal of Infectious Diseases, vol.190, issue.5, pp.971-974, 2004.
DOI : 10.1086/423143

F. Maggi and M. Bendinelli, Immunobiology of the Torque Teno Viruses and Other Anelloviruses, Curr. Top. Microbiol. Immunol, vol.331, pp.65-90, 2009.
DOI : 10.1007/978-3-540-70972-5_5

F. Tsuda, Determination of antibodies to TT virus (TTV) and application to blood donors and patients with post-transfusion non-A to G hepatitis in Japan, Journal of Virological Methods, vol.77, issue.2, pp.199-206, 1999.
DOI : 10.1016/S0166-0934(98)00154-2

. Tsuda, IgM-class antibodies to TT virus (TTV) in patients with acute TTV infection, Hepatology Research, vol.19, issue.1, pp.1-11, 2001.
DOI : 10.1016/S1386-6346(00)00086-3

C. D. Madsen, TTV viral load as a marker for immune reconstitution after initiation of HAART in HIV-infected patients, HIV Clin Trials, vol.3, pp.287-295, 2002.

M. Fogli, Emergence of Exhausted B Cells in Asymptomatic HIV-1-Infected Patients Na??ve for HAART is Related to Reduced Immune Surveillance, Clinical and Developmental Immunology, vol.12, issue.17, pp.1-10, 2012.
DOI : 10.1073/pnas.0901702106

R. Tuveri, Impact of TT virus infection in acute and chronic, viral- and non viral-related liver diseases, Journal of Hepatology, vol.33, issue.1, pp.121-127, 2000.
DOI : 10.1016/S0168-8278(00)80168-3

M. Ishimura, Hepatitis-associated aplastic anemia during a primary infection of genotype 1a torque teno virus, European Journal of Pediatrics, vol.348, issue.7, pp.899-902, 2010.
DOI : 10.1007/s00431-009-1116-8

T. Hussain, S. Manzoor, Y. Waheed, H. Tariq, and K. Hanif, Phylogenetic analysis of torque teno virus genome from Pakistani isolate and incidence of co-infection among HBV/HCV infected patients, Virology Journal, vol.9, issue.1, p.320, 2012.
DOI : 10.1093/bioinformatics/btm404

M. García-Álvarez, Association of torque teno virus (TTV) and torque teno mini virus (TTMV) with liver disease among patients coinfected with human immunodeficiency virus and hepatitis C virus, Eur, J. Clin. Microbiol. Infect. Dis, pp.10-1007, 2012.

P. Kristian, Impact of TTV and SENV infection in chronic hepatitis B or C on liver histology and therapy outcome, Bratisl Lek Listy, vol.111, pp.629-634, 2010.

M. Tsuge, G to A hypermutation of TT virus, Virus Research, vol.149, issue.2, pp.211-216, 2010.
DOI : 10.1016/j.virusres.2010.01.019

M. Irshad, K. Mandal, S. Singh, and S. K. Agarwal, Torque teno virus infection in hemodialysis patients in North India, International Urology and Nephrology, vol.56, issue.Pt 12, pp.1077-1083, 2010.
DOI : 10.1007/s11255-009-9648-4

J. Chung, Small Anellovirus Infections in Korean Children, Emerging Infectious Diseases, vol.13, issue.5, pp.791-793, 2007.
DOI : 10.3201/eid1305.061149

P. Biagini, R. N. Charrel, P. De-micco, and X. De-lamballerie, Association of TT Virus Primary Infection with Rhinitis in a Newborn, Clinical Infectious Diseases, vol.36, issue.1, pp.128-129, 2003.
DOI : 10.1086/345552

T. Kekarainen and J. Segalés, Torque Teno Sus Virus in Pigs: an Emerging Pathogen?, Transboundary and Emerging Diseases, vol.81, 2012.
DOI : 10.1111/j.1865-1682.2011.01289.x

L. Rammohan, Increased prevalence of torque teno viruses in porcine respiratory disease complex affected pigs, Veterinary Microbiology, vol.157, issue.1-2, pp.61-68, 2012.
DOI : 10.1016/j.vetmic.2011.12.013

H. Zur-hausen and E. M. De-villiers, TT Viruses: Oncogenic or Tumor-Suppressive Properties?, Curr. Top. Microbiol. Immunol, vol.331, pp.109-116, 2009.
DOI : 10.1007/978-3-540-70972-5_7

P. Pineau, Effect of TT Virus Infection on Hepatocellular Carcinoma Development: Results of a Euro???Asian Survey, The Journal of Infectious Diseases, vol.181, issue.3, pp.1138-1142, 2000.
DOI : 10.1086/315321

E. Villiers, TTV infection in colorectal cancer tissues and normal mucosa, International Journal of Cancer, vol.66, issue.9, pp.2109-2112, 2007.
DOI : 10.1002/ijc.22931

G. Szládek, High co-prevalence of genogroup 1 TT virus and human papillomavirus is associated with poor clinical outcome of laryngeal carcinoma, Journal of Clinical Pathology, vol.58, issue.4, pp.402-405, 2005.
DOI : 10.1136/jcp.2004.022103

K. Tomasiewicz, R. Modrzewska, A. Lyczak, and G. Krawczuk, TT virus infection and pancreatic cancer: Relationship or accidental coexistence, World Journal of Gastroenterology, vol.11, issue.18, pp.2847-2849, 2005.
DOI : 10.3748/wjg.v11.i18.2847

S. Calcaterra, Cervicovaginal shedding of TT virus in HIV-infected women, J. Hum. Virol, vol.4, pp.343-345, 2001.

C. Girard, High Prevalence of Torque Teno (TT) Virus in Classical Kaposi's Sarcoma, Acta Dermato-Venereologica, vol.87, issue.1, pp.14-17, 2007.
DOI : 10.2340/00015555-0188

E. Fehér, Comparison of diversity of torque teno virus 1 in different mucosal tissues and disorders, Acta Microbiologica et Immunologica Hungarica, vol.58, issue.4, pp.319-337, 2011.
DOI : 10.1556/AMicr.58.2011.4.8

P. and G. Jr, Increased prevalence of transfusion-transmitted virus and cross-reactivity with immunodominant epitopes of the HRES-1/p28 endogenous retroviral autoantigen in patients with systemic lupus erythematosus, Clin. Immunol, vol.116, pp.124-134, 2005.

M. R. Da-costa, I. P. Da-costa, S. Devalle, A. R. De-castro, and S. Z. Freitas, Preval??ncia e diversidade gen??tica do torque teno v??rus em pacientes com l??pus eritematoso sist??mico em servi??o de refer??ncia no Mato Grosso do Sul, Revista Brasileira de Reumatologia, vol.52, issue.1, pp.49-54, 2012.
DOI : 10.1590/S0482-50042012000100006

H. Katano, Pathogenic characterization of a cervical lymph node derived from a patient with Kawasaki disease, Int J Clin Exp Pathol, vol.5, pp.814-823, 2012.

M. Sospedra, Recognition of Conserved Amino Acid Motifs of Common Viruses and Its Role in Autoimmunity, PLoS Pathogens, vol.147, issue.4, p.41, 2005.
DOI : 10.1371/journal.ppat.0010041.st003

J. E. Libbey and R. S. Fujinami, Potential Triggers of MS, Results Probl Cell Differ, vol.51, pp.21-42, 2010.
DOI : 10.1007/400_2008_12

S. Devalle, F. Rua, M. G. Morgado, and C. , Variations in the frequencies of torque teno virus subpopulations during HAART treatment in HIV-1-coinfected patients, Archives of Virology, vol.19, issue.8, pp.1285-1291, 2009.
DOI : 10.1007/s00705-009-0440-7

J. K. Christensen, Prevalence and Prognostic Significance of Infection with TT Virus in Patients Infected with Human Immunodeficiency Virus, The Journal of Infectious Diseases, vol.181, issue.5, pp.1796-1799, 2000.
DOI : 10.1086/315440

P. Biagini, Evolution of Anelloviridae strains distribution in serial blood and biopsy samples from a renal transplant patient, Journal of Medical Virology, vol.70, issue.1, pp.96-98, 2012.
DOI : 10.1002/jmv.22259
URL : https://hal.archives-ouvertes.fr/hal-00679275

G. Szládek, Persisting TT virus (TTV) genogroup 1 variants in renal transplant recipients, Archives of Virology, vol.148, issue.5, pp.841-851, 2003.
DOI : 10.1007/s00705-002-0001-9

E. and M. Tekippe, Increased Prevalence of Anellovirus in Pediatric Patients with Fever, PLoS ONE, vol.7, p.50937, 2012.

N. L. Yozwiak, Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing, PLoS Neglected Tropical Diseases, vol.73, issue.2, p.1485, 2012.
DOI : 10.1371/journal.pntd.0001485.s004

P. Simmonds, TT Virus???Part of the Normal Human Flora?, The Journal of Infectious Diseases, vol.180, issue.5, pp.1748-1750, 1999.
DOI : 10.1086/315103

S. Li, Detection and identification of plasma bacterial and viral elements in HIV/AIDS patients in comparison to healthy adults, Clinical Microbiology and Infection, vol.18, issue.11, pp.1126-1133, 2012.
DOI : 10.1111/j.1469-0691.2011.03690.x

J. Telles, Viral and bacterial pathogens identification in children hospitalised for severe pneumonia and parapneumonic empyema, pneumonia: A Peer Reviewed Open Access Journal, vol.1, issue.0, pp.11-19, 2012.
DOI : 10.15172/pneu.2012.1/228

N. Richard, The Impact of Dual Viral Infection in Infants Admitted to a Pediatric Intensive Care Unit Associated with Severe Bronchiolitis, The Pediatric Infectious Disease Journal, vol.27, issue.3, pp.213-217, 2008.
DOI : 10.1097/INF.0b013e31815b4935

G. Paranhos-baccalà, Mixed Respiratory Virus Infections, Journal of Clinical Virology, vol.43, issue.4, pp.407-410, 2008.
DOI : 10.1016/j.jcv.2008.08.010

A. Desrumaux, ??pid??miologie et??caract??ristiques cliniques des??complications suppuratives des??pneumonies de??l'enfant, Archives de P??diatrie, vol.14, issue.11, pp.1298-1303, 2007.
DOI : 10.1016/j.arcped.2007.06.008

K. D. Schultz, The Changing Face of Pleural Empyemas in Children: Epidemiology and Management, PEDIATRICS, vol.113, issue.6, pp.1735-1740, 2004.
DOI : 10.1542/peds.113.6.1735

R. Gupta and S. Crowley, Increasing paediatric empyema admissions, Thorax, vol.61, issue.2, pp.179-180, 2006.
DOI : 10.1136/thx.2005.049510

E. Paraskakis, E. Vergadi, A. Chatzimichael, and D. Bouros, Current evidence for the management of paediatric parapneumonic effusions, Current Medical Research and Opinion, vol.28, issue.7, pp.1179-1192, 2012.
DOI : 10.1185/03007995.2012.684674

P. Mangeot, High Levels of Transduction of Human Dendritic Cells with Optimized SIV Vectors, Molecular Therapy, vol.5, issue.3, pp.283-290, 2002.
DOI : 10.1006/mthe.2002.0541

F. Faurez, D. Dory, A. Henry, S. Bougeard, and A. Jestin, Replication efficiency of rolling-circle replicon-based plasmids derived from porcine circovirus 2 in eukaryotic cells, Journal of Virological Methods, vol.165, issue.1, pp.27-35, 2010.
DOI : 10.1016/j.jviromet.2009.12.013
URL : https://hal.archives-ouvertes.fr/hal-00493407

S. A. Bustin, The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments, Clinical Chemistry, vol.55, issue.4, pp.611-622, 2009.
DOI : 10.1373/clinchem.2008.112797

R. W. Light, Parapneumonic Effusions and Empyema, Proceedings of the American Thoracic Society, vol.3, issue.1, pp.75-80, 2006.
DOI : 10.1513/pats.200510-113JH

S. F. Thijsen, R. Luderer, J. M. Van-gorp, S. J. Oudejans, and A. W. Bossink, A possible role for Epstein-Barr virus in the pathogenesis of pleural effusion, European Respiratory Journal, vol.26, issue.4, pp.662-666, 2005.
DOI : 10.1183/09031936.05.00131204

C. Meyers, T. J. Mayer, and M. A. Ozbun, Synthesis of infectious human papillomavirus type 18 in differentiating epithelium transfected with viral DNA, J. Virol, vol.71, pp.7381-7386, 1997.

K. A. Foster, C. G. Oster, M. M. Mayer, M. L. Avery, and K. L. Audus, Characterization of the A549 Cell Line as a Type II Pulmonary Epithelial Cell Model for Drug Metabolism, Experimental Cell Research, vol.243, issue.2, pp.359-366, 1998.
DOI : 10.1006/excr.1998.4172

H. Bernard, I. E. Calleja-macias, and S. T. Dunn, Genome variation of human papillomavirus types: Phylogenetic and medical implications, International Journal of Cancer, vol.168, issue.5, pp.1071-1076, 2006.
DOI : 10.1002/ijc.21655

D. Todd, M. S. Mcnulty, B. M. Adair, and G. M. Allan, Animal circoviruses, Animal circoviruses, Adv. Virus Res, vol.57, pp.1-70, 2001.
DOI : 10.1016/S0065-3527(01)57000-1

R. J. Mason, Biology of alveolar type II cells, Respirology, vol.115, issue.s1, pp.12-15, 2006.
DOI : 10.1165/rcmb.2005-0063OC

S. Wu, J. P. Metcalf, and W. Wu, Innate immune response to influenza virus, Current Opinion in Infectious Diseases, vol.24, issue.3, pp.235-240, 2011.
DOI : 10.1097/QCO.0b013e328344c0e3

F. Maggi, TT Virus Loads and Lymphocyte Subpopulations in Children with Acute Respiratory Diseases, Journal of Virology, vol.77, issue.16, pp.9081-9083, 2003.
DOI : 10.1128/JVI.77.16.9081-9083.2003

W. C. Russell, Adenoviruses: update on structure and function, Journal of General Virology, vol.90, issue.1, pp.1-20, 2009.
DOI : 10.1099/vir.0.003087-0

L. N. Sørensen, TLR2 and TLR9 Synergistically Control Herpes Simplex Virus Infection in the Brain, The Journal of Immunology, vol.181, issue.12, pp.8604-8612, 2008.
DOI : 10.4049/jimmunol.181.12.8604

S. Ruan, Interleukin-12 and Host Defense against Murine Pneumocystis Pneumonia, Infection and Immunity, vol.76, issue.5, pp.2130-2137, 2008.
DOI : 10.1128/IAI.00065-08

C. Mathieu, Lethal Nipah Virus Infection Induces Rapid Overexpression of CXCL10, PLoS ONE, vol.55, issue.2, 2012.
DOI : 10.1371/journal.pone.0032157.s002
URL : https://hal.archives-ouvertes.fr/hal-00965605

T. Bouwmeester, A physical and functional map of the human TNF-??/NF-??B signal transduction pathway, Nature Cell Biology, vol.9, issue.2, pp.97-105, 2004.
DOI : 10.1021/ac950914h

S. Beinke, M. J. Robinson, M. Hugunin, and S. C. Ley, Lipopolysaccharide Activation of the TPL-2/MEK/Extracellular Signal-Regulated Kinase Mitogen-Activated Protein Kinase Cascade Is Regulated by I??B Kinase-Induced Proteolysis of NF-??B1 p105, Molecular and Cellular Biology, vol.24, issue.21, pp.9658-9667, 2004.
DOI : 10.1128/MCB.24.21.9658-9667.2004

M. Vougioukalaki, D. C. Kanellis, K. Gkouskou, and A. G. Eliopoulos, Tpl2 kinase signal transduction in inflammation and cancer, Cancer Letters, vol.304, issue.2, pp.80-89, 2011.
DOI : 10.1016/j.canlet.2011.02.004

T. Lammers and S. Lavi, Role of Type 2C Protein Phosphatases in Growth Regulation and in Cellular Stress Signaling, Critical Reviews in Biochemistry and Molecular Biology, vol.6, issue.6, pp.437-461, 2007.
DOI : 10.1074/jbc.M203969200

S. Tamura, PP2C family members play key roles in regulation of cell survival and apoptosis, Cancer Sci, pp.563-567, 2006.

J. Guergnon, PP2A targeting by viral proteins: A widespread biological strategy from DNA/RNA tumor viruses to HIV-1, Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, vol.1812, issue.11, pp.1498-1507, 2011.
DOI : 10.1016/j.bbadis.2011.07.001
URL : https://hal.archives-ouvertes.fr/pasteur-00649918

M. Dai and H. Lu, Inhibition of MDM2-mediated p53 Ubiquitination and Degradation by Ribosomal Protein L5, Journal of Biological Chemistry, vol.279, issue.43, pp.44475-44482, 2004.
DOI : 10.1074/jbc.M403722200

M. Zhang, L. Wang, C. Chen, Y. Yang, and L. Zhang, Role of dendritic cells in the pathogenesis of severe pneumonia in children, Zhonghua Er Ke Za Zhi, vol.43, pp.410-413, 2005.

H. M. Friedman, Immune evasion by herpes simplex virus type 1, strategies for virus survival, Trans Am Clin Climatol Assoc, vol.114, pp.103-112, 2003.

I. L. Dodge, M. W. Carr, M. Cernadas, and M. B. Brenner, IL-6 Production by Pulmonary Dendritic Cells Impedes Th1 Immune Responses, The Journal of Immunology, vol.170, issue.9, pp.4457-4464, 2003.
DOI : 10.4049/jimmunol.170.9.4457

D. J. Cua and C. M. Tato, Innate IL-17-producing cells: the sentinels of the immune system, Nature Reviews Immunology, vol.31, issue.7, pp.479-489, 2010.
DOI : 10.1038/nri2800

H. Hackstein and A. W. Thomson, Dendritic cells: emerging pharmacological targets of immunosuppressive drugs, Nature Reviews Immunology, vol.4, issue.1, pp.24-34, 2004.
DOI : 10.1038/nri1256

M. E. Rothenberg and S. P. Hogan, THE EOSINOPHIL, Annual Review of Immunology, vol.24, issue.1, pp.147-174, 2006.
DOI : 10.1146/annurev.immunol.24.021605.090720

G. L. Rogers, Innate Immune Responses to AAV Vectors, Frontiers in Microbiology, vol.2, issue.2, p.194, 2011.
DOI : 10.3389/fmicb.2011.00194

M. J. Walter, N. Kajiwara, P. Karanja, M. Castro, and M. J. Holtzman, Interleukin 12 P40 Production by Barrier Epithelial Cells during Airway Inflammation, The Journal of Experimental Medicine, vol.135, issue.3, pp.339-351, 2001.
DOI : 10.1016/0091-6749(87)90129-1

A. D. Lehmann, An in vitro triple cell co-culture model with primary cells mimicking the human alveolar epithelial barrier, European Journal of Pharmaceutics and Biopharmaceutics, vol.77, issue.3, pp.398-406, 2011.
DOI : 10.1016/j.ejpb.2010.10.014

B. Rothen-rutishauser, F. Blank, C. Mühlfeld, and P. Gehr, models of the human epithelial airway barrier to study the toxic potential of particulate matter, Expert Opinion on Drug Metabolism & Toxicology, vol.6, issue.8, pp.1075-1089, 2008.
DOI : 10.1586/17476348.2.2.215

T. M. Rivers, Viruses and Koch's Postulates, J. Bacteriol, vol.33, pp.1-12, 1937.

R. La-pneumonie-est-la, Elle peut être provoquée par un certain nombre d'agents pathogènes connus mais 15 à 35% des pneumonies de l'enfant restent encore non renseignées d'un point de vue étiologique. L'utilisation d'un test moléculaire de découverte de nouveaux pathogènes nous a permis de découvrir de nouvelles espèces de Torque Teno Mini Virus (TTMV, Anelloviridae), nommées TTMV-LY, dans trois épanchements pleuraux provenant d'enfants hospitalisés avec une pleuro-pneumopathie

L. Génomes-complets-de and T. Ont-Été-isolés, caractérisés puis répliqués in vitro. La réponse des cellules épithéliales alvéolaires, ainsi que des cellules présentatrices d'antigènes (CPA), impliquées dans l'inflammation, a été étudiée après infection par les virions néo-synthétisés