C. A. Glaser, S. Honarmand, and L. J. Anderson, Beyond viruses: clinical profiles and etiologies associated with encephalitis, Clin Infect Dis Off Publ Infect Dis Soc Am, vol.43, pp.1565-1577, 2006.

A. Venkatesan, A. R. Tunkel, and K. C. Bloch, Case definitions, diagnostic algorithms, and priorities in encephalitis: consensus statement of the international encephalitis consortium, Clin Infect Dis Off Publ Infect Dis Soc Am, vol.57, pp.1114-1128, 2013.

A. Mailles, J. Stahl, and K. C. Bloch, Update and new insights in encephalitis, Clin Microbiol Infect Off Publ Eur Soc Clin Microbiol Infect Dis, vol.23, pp.607-613, 2017.

W. J. Tabachnick, Climate Change and the Arboviruses: Lessons from the Evolution of the Dengue and Yellow Fever Viruses, Annu Rev Virol, vol.3, pp.125-145, 2016.

U. Ashraf, J. Ye, X. Ruan, S. Wan, B. Zhu et al., Usutu virus: an emerging flavivirus in Europe, Viruses, vol.7, pp.219-238, 2015.

, International Committee on Taxonomy of Viruses (ICTV)

C. N. Dandawate, P. K. Rajagopalan, K. M. Pavri, and T. H. Work, Virus isolations from mosquitoes collected in North Arcot district, Madras state, and Chittoor district, Indian J Med Res, vol.57, pp.1420-1426, 1955.

H. Salimi, M. D. Cain, and R. S. Klein, Encephalitic Arboviruses: Emergence, Clinical Presentation, and Neuropathogenesis, Neurother J Am Soc Exp Neurother, vol.13, pp.514-534, 2016.

R. L. Doherty, J. G. Carley, B. H. Kay, C. Filippich, E. N. Marks et al., Isolation of virus strains from mosquitoes collected in Queensland, 1972-1976, Aust J Exp Biol Med Sci, vol.57, pp.509-520, 1979.

R. L. Doherty, J. G. Carley, M. J. Mackerras, and E. N. Marks, Studies of arthropod-borne virus infections in Queensland. III. Isolation and characterization of virus strains from wild-caught mosquitoes in North Queensland, Aust J Exp Biol Med Sci, vol.41, pp.17-39, 1963.

A. M. Shchetinin, D. K. Lvov, and P. G. Deriabin, Genetic and Phylogenetic Characterization of Tataguine and Witwatersrand Viruses and Other Orthobunyaviruses of the Anopheles A, Viruses, vol.7, pp.5987-6008, 2015.

V. Palya, E. W. Kovács, and S. Marton, Novel Orthobunyavirus Causing Severe Kidney Disease in Broiler Chickens, Emerg Infect Dis, vol.25, pp.1110-1117, 2014.

A. Miller, R. Carchman, R. Long, and S. A. Denslow, La Crosse viral infection in hospitalized pediatric patients in Western North Carolina, Hosp Pediatr, vol.2, pp.235-242, 2012.

E. S. Reynolds, C. E. Hart, M. E. Hermance, D. L. Brining, and S. Thangamani, An Overview of Animal Models for Arthropod-Borne Viruses, Comp Med, vol.67, pp.232-241, 2017.

J. Hellert, A. Aebischer, and K. Wernike, Orthobunyavirus spike architecture and recognition by neutralizing antibodies, Nat Commun, vol.10, p.879, 2019.

A. Dubot-pérès, O. Sengvilaipaseuth, A. Chanthongthip, P. N. Newton, and X. De-lamballerie, How many patients with anti-JEV IgM in cerebrospinal fluid really have Japanese encephalitis?, Lancet Infect Dis, vol.15, pp.1376-1377, 2015.

S. Touch, S. Hills, and B. Sokhal, Epidemiology and burden of disease from Japanese encephalitis in Cambodia: results from two years of sentinel surveillance, Trop Med Int Health TM IH, vol.14, pp.1365-1373, 2009.

M. R. Wilson, D. Suan, and A. Duggins, A novel cause of chronic viral meningoencephalitis: Cache Valley virus, Ann Neurol, vol.82, p.61, 2017.

, Umbre orthobunyavirus strain Marna (Case #2) 61.1 61.1 64.2 62.1 57, vol.9

L. Peckeu, N. Delasnerie-lauprètre, and J. Brandel, Accuracy of diagnosis criteria in patients with suspected diagnosis of sporadic Creutzfeldt-Jakob disease and detection of 14-3-3 protein, Euro Surveill Bull Eur Sur Mal Transm Eur Commun Dis Bull, vol.22, 1992.
URL : https://hal.archives-ouvertes.fr/hal-01622173

C. I. Lasmézas, J. P. Deslys, and O. Robain, Transmission of the BSE agent to mice in the absence of detectable abnormal prion protein, Science, vol.275, pp.402-405, 1997.

A. Criscuolo and S. Brisse, AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads, Genomics, vol.102, pp.500-506, 2013.

D. Li, C. Liu, R. Luo, K. Sadakane, and T. Lam, MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinforma Oxf Engl, vol.31, pp.1674-1676, 2015.

T. Bigot, S. Temmam, P. Pérot, and M. Eloit, RVDB-prot, a reference viral protein database and its HMM profiles, F1000Research, vol.8, p.530, 2019.

B. Buchfink, C. Xie, and D. H. Huson, Fast and sensitive protein alignment using DIAMOND, Nat Methods, vol.12, pp.59-60, 2015.

D. E. Wood and S. L. Salzberg, Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome Biol, vol.15, p.46, 2014.

D. Kim, L. Song, F. P. Breitwieser, and S. L. Salzberg, Centrifuge: rapid and sensitive classification of metagenomic sequences, Genome Res, 2016.

D. T. Truong, E. A. Franzosa, and T. L. Tickle, MetaPhlAn2 for enhanced metagenomic taxonomic profiling, Nat Methods, vol.12, pp.902-903, 2015.

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res, vol.30, pp.3059-3066, 2002.

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, pp.772-780, 2013.

M. Kearse, R. Moir, and A. Wilson, Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinforma Oxf Engl, vol.28, pp.1647-1649, 2012.

S. Kumar, G. Stecher, and K. Tamura, MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets, Mol Biol Evol, vol.33, pp.1870-1874, 2016.

T. Iwaki, M. Figuera, V. A. Ploplis, and F. J. Castellino, Rapid selection of Drosophila S2 cells with the puromycin resistance gene, BioTechniques, vol.35, p.486, 2003.

T. Ducomble, H. Wilking, and K. Stark, Lack of evidence for Schmallenberg virus infection in highly exposed persons, Emerg Infect Dis, vol.18, pp.1333-1335, 2012.

C. Reusken, C. Van-den-wijngaard, and P. Van-beek, Lack of evidence for zoonotic transmission of Schmallenberg virus, Emerg Infect Dis, vol.18, pp.1746-1754, 2012.

M. Eiden, P. Gil, and U. Ziegler, Emergence of two Usutu virus lineages in Culex pipiens mosquitoes in the Camargue, Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis, vol.61, pp.151-154, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01890103

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, pp.357-359, 2012.