D. Ecker, R. Sampath, C. Massire, L. Blyn, T. Hall et al., Ibis T5000: a universal biosensor approach for microbiology, Nature Reviews Microbiology, vol.44, issue.7, pp.553-558, 2008.
DOI : 10.1038/nrmicro1918

P. Gyarmati, T. Conze, S. Zohari, N. Leblanc, M. Nilsson et al., Simultaneous Genotyping of All Hemagglutinin and Neuraminidase Subtypes of Avian Influenza Viruses by Use of Padlock Probes, Journal of Clinical Microbiology, vol.46, issue.5, pp.461747-1751, 2008.
DOI : 10.1128/JCM.02292-07

E. Ghedin, A. Pumfery, C. De-la-fuente, K. Yao, N. Miller et al., Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis, Retrovirology, vol.1, issue.1, p.10, 2004.
DOI : 10.1186/1742-4690-1-10

Z. Sun, W. Zheng, X. Mao, B. Zhang, L. Lu et al., Rapid preparation of DNA microarray using PCR for hepatitis B and D virus detection, pp.677-679, 2003.

Z. Sun, W. Zheng, B. Zhang, L. Lu, X. Mao et al., Detection of hepatitis D virus by cDNA microarray method, Hepatobiliary Pancreat Dis Int, vol.3, issue.3, pp.423-427, 2004.

Y. Song, E. Dai, J. Wang, H. Liu, J. Zhai et al., Genotyping of hepatitis B virus (HBV) by oligonucleotides microarray, Molecular and Cellular Probes, vol.20, issue.2, pp.121-127, 2006.
DOI : 10.1016/j.mcp.2005.11.004

C. Klaassen, C. Prinsen, H. De-valk, A. Horrevorts, M. Jeunink et al., DNA Microarray Format for Detection and Subtyping of Human Papillomavirus, Journal of Clinical Microbiology, vol.42, issue.5, pp.2152-2160, 2004.
DOI : 10.1128/JCM.42.5.2152-2160.2004

S. Honma, V. Chizhikov, N. Santos, M. Tatsumi, T. Mdo et al., Development and validation of DNA microarray for genotyping group A rotavirus VP4, ], and P[14]) and VP7 (G1 to G6, G8 to G10, and G12) genes, pp.452641-2648, 2007.

Y. Wang, W. Ma, X. Mao, Q. Wu, L. Li et al., Design and preparation of oligonucleotide microarray for vaccinia virus detection, pp.180-183, 2004.

J. Korimbocus, N. Scaramozzino, B. Lacroix, J. Crance, D. Garin et al., DNA Probe Array for the Simultaneous Identification of Herpesviruses, Enteroviruses, and Flaviviruses, Journal of Clinical Microbiology, vol.43, issue.8, pp.433779-3787, 2005.
DOI : 10.1128/JCM.43.8.3779-3787.2005

A. Neverov, M. Riddell, W. Moss, D. Volokhov, P. Rota et al., Genotyping of Measles Virus in Clinical Specimens on the Basis of Oligonucleotide Microarray Hybridization Patterns, Journal of Clinical Microbiology, vol.44, issue.10, pp.443752-3759, 2006.
DOI : 10.1128/JCM.00998-06

B. Lin, Z. Wang, G. Vora, J. Thornton, J. Schnur et al., 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

T. Leski, B. Lin, A. Malanoski, Z. Wang, N. Long et al., Testing and Validation of High Density Resequencing Microarray for Broad Range Biothreat Agents Detection, PLoS ONE, vol.14, issue.8, p.6569, 2009.
DOI : 10.1371/journal.pone.0006569.s006

N. Berthet, A. Reinhardt, I. Leclercq, S. Van-ooyen, C. Batejat et al., 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

G. Palacios, P. Quan, O. Jabado, S. Conlan, D. Hirschberg et al., Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases, Emerging Infectious Diseases, vol.13, issue.1, pp.73-81, 2007.
DOI : 10.3201/eid1301.060837

D. Wang, L. Coscoy, M. Zylberberg, P. Avila, H. Boushey et al., Microarray-based detection and genotyping of viral pathogens, Proc Natl Acad Sci, issue.24, pp.9915687-15692, 2002.

D. Wang, A. Urisman, Y. Liu, M. Springer, T. Ksiazek et al., Viral Discovery and Sequence Recovery Using DNA Microarrays, PLoS Biology, vol.99, issue.2, p.2, 2003.
DOI : 10.1371/journal.pbio.0000002.st002

E. Dawson, C. Moore, D. Dankbar, M. Mehlmann, M. Townsend et al., Identification of A/H5N1 Influenza Viruses Using a Single Gene Diagnostic Microarray, Analytical Chemistry, vol.79, issue.1, pp.378-384, 2007.
DOI : 10.1021/ac061920o

D. Dankbar, E. Dawson, M. Mehlmann, C. Moore, J. Smagala et al., Diagnostic Microarray for Influenza B Viruses, Analytical Chemistry, vol.79, issue.5, pp.2084-2090, 2007.
DOI : 10.1021/ac061960s

M. Townsend, E. Dawson, M. Mehlmann, J. Smagala, D. Dankbar et al., Experimental Evaluation of the FluChip Diagnostic Microarray for Influenza Virus Surveillance, Journal of Clinical Microbiology, vol.44, issue.8, pp.442863-2871, 2006.
DOI : 10.1128/JCM.00134-06

E. Dawson, C. Moore, J. Smagala, D. Dankbar, M. Mehlmann et al., MChip:?? A Tool for Influenza Surveillance, Analytical Chemistry, vol.78, issue.22, pp.787610-7615, 2006.
DOI : 10.1021/ac061739f

J. Li, S. Chen, and D. Evans, Typing and Subtyping Influenza Virus Using DNA Microarrays and Multiplex Reverse Transcriptase PCR, Journal of Clinical Microbiology, vol.39, issue.2, pp.696-704, 2001.
DOI : 10.1128/JCM.39.2.696-704.2001

X. Han, X. Lin, B. Liu, Y. Hou, J. Huang et al., Simultaneously subtyping of all influenza A viruses using DNA microarrays, Journal of Virological Methods, vol.152, issue.1-2, pp.117-121, 2008.
DOI : 10.1016/j.jviromet.2008.05.027

R. Liu, M. Lodes, T. Nguyen, T. Siuda, M. Slota et al., Validation of A Fully Integrated Microfluidic Array Device for Influenza A Subtype Identification and Sequencing, Analytical Chemistry, vol.78, issue.12, pp.784184-4193, 2006.
DOI : 10.1021/ac060450v

M. Lodes, D. Suciu, M. Elliott, A. Stover, M. Ross et al., Use of Semiconductor-Based Oligonucleotide Microarrays for Influenza A Virus Subtype Identification and Sequencing, Journal of Clinical Microbiology, vol.44, issue.4, pp.1209-1218, 2006.
DOI : 10.1128/JCM.44.4.1209-1218.2006

Z. Wang, A. Malanoski, B. Lin, C. Kidd, N. Long et al., Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses, BMC Genomics, vol.9, issue.1, p.577, 2008.
DOI : 10.1186/1471-2164-9-577

Z. Wang, L. Daum, G. Vora, D. Metzgar, E. Walter et al., Identifying Influenza Viruses with Resequencing Microarrays, Emerging Infectious Diseases, vol.12, issue.4, pp.638-646, 2006.
DOI : 10.3201/eid1204.051441

B. Lin, K. Blaney, A. Malanoski, A. Ligler, J. Schnur et al., Using a Resequencing Microarray as a Multiple Respiratory Pathogen Detection Assay, Journal of Clinical Microbiology, vol.45, issue.2, pp.443-452, 2007.
DOI : 10.1128/JCM.01870-06

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1829030

B. Lin, A. Malanoski, Z. Wang, K. Blaney, N. Long et al., Universal Detection and Identification of Avian Influenza Virus by Use of Resequencing Microarrays, Journal of Clinical Microbiology, vol.47, issue.4, pp.988-993, 2009.
DOI : 10.1128/JCM.01346-08

A. Malanoski, B. Lin, and D. Stenger, A model of base-call resolution on broad-spectrum pathogen detection resequencing DNA microarrays, Nucleic Acids Research, vol.36, issue.10, pp.3194-3201, 2008.
DOI : 10.1093/nar/gkm1156

L. Dacheux, N. Berthet, G. Dissard, E. Holmes, O. Delmas et al., Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses, Journal of Virology, vol.84, issue.18, pp.9557-9574
DOI : 10.1128/JVI.00771-10

URL : https://hal.archives-ouvertes.fr/pasteur-00507428

R. Webster, W. Bean, O. Gorman, T. Chambers, and Y. Kawaoka, Evolution and ecology of influenza A viruses, Microbiol Rev, vol.56, issue.1, pp.152-179, 1992.

D. Cutler, M. Zwick, M. Carrasquillo, C. Yohn, K. Tobin et al., High-throughput variation detection and genotyping using microarrays, Genome Res, issue.11, pp.111913-1925, 2001.

C. Russell, T. Jones, I. Barr, N. Cox, R. Garten et al., The Global Circulation of Seasonal Influenza A (H3N2) Viruses, Science, vol.320, issue.5874, pp.320340-346, 2008.
DOI : 10.1126/science.1154137

R. Zell, S. Motzke, A. Krumbholz, P. Wutzler, V. Herwig et al., Novel reassortant of swine influenza H1N2 virus in Germany, Journal of General Virology, vol.89, issue.1, pp.271-276, 2008.
DOI : 10.1099/vir.0.83338-0

M. Castrucci, I. Donatelli, L. Sidoli, G. Barigazzi, Y. Kawaoka et al., Genetic Reassortment between Avian and Human Influenza A Viruses in Italian Pigs, Virology, vol.193, issue.1, pp.503-506, 1993.
DOI : 10.1006/viro.1993.1155

R. Pyhala and R. Visakorpi, Influenza A(H1N1) viruses of the 1977/78 outbreak: isolation and haemagglutination properties, J Hyg (Lond), vol.1979, issue.821, pp.81-88

N. Berthet, I. Leclercq, A. Dublineau, S. Shigematsu, A. Burguiere et al., High-density resequencing DNA microarrays in public health emergencies, Nature Biotechnology, vol.11, issue.1, pp.25-27, 2010.
DOI : 10.1038/nbt0110-25

URL : https://hal.archives-ouvertes.fr/pasteur-00460127

W. Dowdle, A. Kendal, and G. Noble, Influenza viruses, Diagnostic Procedures for Viral, Rickettsial and Chlamydial Infections, pp.585-609, 1979.

N. Berthet, P. Dickinson, I. Filliol, A. Reinhardt, C. Batejat et al., Massively parallel pathogen identification using high-density microarrays, Microbial Biotechnology, vol.14, issue.0, pp.79-86, 2008.
DOI : 10.1186/gb-2004-6-1-r10

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.253389-3402, 1997.
DOI : 10.1093/nar/25.17.3389