Comparative analysis of qRT-PCR and TCID50 assays ,
Primers and probes used for the real time RT-PCR assays ,
List of 85 TBEV sequences retrieved from GenBank ,
List of 56 TBFV sequences retrieved from GenBank ,
Results of weighing of challenged mice at days 11 and 12 post-challenge ,
Re-encoded sequence (corresponding to positions 8, pp.619-629 ,
Pathogenic flaviviruses, The Lancet, vol.371, issue.9611, pp.500-509, 2008. ,
DOI : 10.1016/S0140-6736(08)60238-X
Flaviviruses: Past, Present and Future. Molecular Virology and Control of Flaviviruses, pp.1-7, 2012. ,
Non-canonical translation in RNA viruses, Journal of General Virology, vol.93, issue.Pt_7, pp.1385-1409, 2012. ,
DOI : 10.1099/vir.0.042499-0
A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting, Virology Journal, vol.6, issue.1, 2009. ,
DOI : 10.1186/1743-422X-6-14
A multigene analysis of the phylogenetic relationships among the flaviviruses (Family: Flaviviridae) and the evolution of vector transmission, Archives of Virology, vol.93, issue.2, pp.309-325, 2006. ,
DOI : 10.1007/s00705-005-0626-6
Genetic characterization of tick-borne flaviviruses: New insights into evolution, pathogenetic determinants and taxonomy, Virology, vol.361, issue.1, pp.80-92, 2007. ,
DOI : 10.1016/j.virol.2006.09.015
Tick-borne virus diseases of human interest in Europe, Clinical Microbiology and Infection, vol.10, issue.12, pp.1040-1055, 2004. ,
DOI : 10.1111/j.1469-0691.2004.01022.x
Sequence analysis and genetic classification of tick-borne encephalitis viruses from Europe and Asia., Journal of General Virology, vol.80, issue.1, pp.179-185, 1999. ,
DOI : 10.1099/0022-1317-80-1-179
Tick-borne encephalitis, Antiviral Research, vol.57, issue.1-2, pp.129-146, 2003. ,
DOI : 10.1016/S0166-3542(02)00206-1
Main features of tick-borne encephalitis eco-epidemiology in Russia, Zentralblatt f??r Bakteriologie, vol.289, issue.5-7, pp.525-539, 1999. ,
DOI : 10.1016/S0934-8840(99)80006-1
Tick-borne Encephalitis Vaccines, Journal of Bioterrorism & Biodefense, vol.01, issue.01, pp.3-23997980, 2011. ,
DOI : 10.4172/2157-2526.S1-003
Tick-borne encephalitis increasing in Sweden, Euro Surveill, vol.16, 2011. ,
Tick-borne encephalitis in Europe and beyond?the epidemiological situation as of, Euro Surveill, vol.13, 2007. ,
The current perspective on tick-borne encephalitis awareness and prevention in six Central and Eastern European countries: Report from a meeting of experts convened to discuss TBE in their region, Vaccine, vol.29, issue.28, pp.4556-4564, 2011. ,
DOI : 10.1016/j.vaccine.2011.04.061
Flaviviruses and flavivirus vaccines, Vaccine, vol.30, issue.29, pp.4301-4306, 2012. ,
DOI : 10.1016/j.vaccine.2011.09.114
Current Status of Flavivirus Vaccines, Annals of the New York Academy of Sciences, vol.4, issue.Suppl. 2, pp.262-271, 2001. ,
DOI : 10.1111/j.1749-6632.2001.tb02702.x
Viscerotropic and neurotropic disease following vaccination with the 17D yellow fever vaccine, ARILVAX??, Vaccine, vol.22, issue.17-18, pp.2103-2105, 2004. ,
DOI : 10.1016/j.vaccine.2004.01.026
Refining the Balance of Attenuation and Immunogenicity of Respiratory Syncytial Virus by Targeted Codon Deoptimization of Virulence Genes, mBio, vol.5, issue.5, 2014. ,
DOI : 10.1128/mBio.01704-14
Attenuation of human respiratory syncytial virus by genome-scale codon-pair deoptimization, Proceedings of the National Academy of Sciences, vol.111, issue.36, pp.13169-13174, 2014. ,
DOI : 10.1073/pnas.1411290111
Computer-aided codon-pairs deoptimization of the major envelope GP5 gene attenuates porcine reproductive and respiratory syndrome virus, Virology, vol.450, issue.451, pp.450-451, 2014. ,
DOI : 10.1016/j.virol.2013.12.009
Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture, Retrovirology, vol.10, issue.1, p.23885919, 2013. ,
DOI : 10.1128/JVI.01594-06
Modulation of Poliovirus Replicative Fitness in HeLa Cells by Deoptimization of Synonymous Codon Usage in the Capsid Region, Journal of Virology, vol.80, issue.7, pp.3259-3272, 2006. ,
DOI : 10.1128/JVI.80.7.3259-3272.2006
Reduction of the Rate of Poliovirus Protein Synthesis through Large-Scale Codon Deoptimization Causes Attenuation of Viral Virulence by Lowering Specific Infectivity, Journal of Virology, vol.80, issue.19, pp.9687-9696, 2006. ,
DOI : 10.1128/JVI.00738-06
Virus Attenuation by Genome-Scale Changes in Codon Pair Bias, Science, vol.320, issue.5884, pp.1784-1787, 2008. ,
DOI : 10.1126/science.1155761
Live attenuated influenza virus vaccines by computer-aided rational design, Nature Biotechnology, vol.79, issue.7, pp.723-726, 2010. ,
DOI : 10.1038/nbt.1636
Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons, Journal of Virology, vol.83, issue.19, pp.9957-9969, 2009. ,
DOI : 10.1128/JVI.00508-09
Random Codon Re-encoding Induces Stable Reduction of Replicative Fitness of Chikungunya Virus in Primate and Mosquito Cells, PLoS Pathogens, vol.79, issue.Pt 11, 2013. ,
DOI : 10.1371/journal.ppat.1003172.s003
Codon usage between genomes is constrained by genome-wide mutational processes, Proceedings of the National Academy of Sciences, vol.101, issue.10, pp.3480-3485, 2004. ,
DOI : 10.1073/pnas.0307827100
Architecture and secondary structure of an entire HIV-1 RNA genome, Nature, vol.14, issue.7256, pp.711-716, 2009. ,
DOI : 10.1038/nature08237
Conserved RNA secondary structures in Flaviviridae genomes, Journal of General Virology, vol.85, issue.5, pp.1113-1124, 2004. ,
DOI : 10.1099/vir.0.19462-0
Flavivirus Capsid Is a Dimeric Alpha-Helical Protein, Journal of Virology, vol.77, issue.12, pp.7143-7149, 2003. ,
DOI : 10.1128/JVI.77.12.7143-7149.2003
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC156156
Slow Fitness Recovery in a Codon-Modified Viral Genome, Molecular Biology and Evolution, vol.29, issue.10, pp.2997-3004, 2012. ,
DOI : 10.1093/molbev/mss119
A case of tick-borne encephalitis in Japan and isolation of the the virus, J Clin Microbiol, vol.35, pp.1943-1947, 1997. ,
Amino acid changes responsible for attenuation of virus neurovirulence in an infectious cDNA clone of the Oshima strain of Tick-borne encephalitis virus, Journal of General Virology, vol.85, issue.4, pp.1007-1018, 2004. ,
DOI : 10.1099/vir.0.19668-0
Clinical evaluation of highly pathogenic tick-borne flavivirus infection in the mouse model, Journal of Medical Virology, vol.3, issue.7, pp.1261-1269, 2009. ,
DOI : 10.1002/jmv.21524
Mortality following peripheral infection with Tick-borne encephalitis virus results from a combination of central nervous system pathology, systemic inflammatory and stress responses, Virology, vol.390, issue.1, 2009. ,
DOI : 10.1016/j.virol.2009.04.026
Flavivirus Encephalitis, Veterinary Pathology, vol.22, issue.5, pp.806-818, 2010. ,
DOI : 10.1177/104063870401600413
URL : http://eprints.lib.hokudai.ac.jp/dspace/bitstream/2115/47038/1/VP47-5_806-818.pdf
Natural Tick-Borne Encephalitis Virus Infection among Wild Small Mammals in the Southeastern Part of Western Siberia, Russia, Vector-Borne and Zoonotic Diseases, vol.6, issue.1, pp.32-41, 2006. ,
DOI : 10.1089/vbz.2006.6.32
The role of small rodents and hedgehogs in a natural focus of tick-borne encephalitis, Bull World Health Organ, vol.36, pp.61-66, 1967. ,
Infection and Injury of Neurons by West Nile Encephalitis Virus, Journal of Virology, vol.77, issue.24, pp.13203-13213, 2003. ,
DOI : 10.1128/JVI.77.24.13203-13213.2003
Morphological changes in human neural cells following tick-borne encephalitis virus infection, Journal of General Virology, vol.90, issue.7, pp.1649-1658, 2009. ,
DOI : 10.1099/vir.0.010058-0
Protective role of TNF-alpha, IL-10 and IL-2 in mice infected with the Oshima strain of Tick-borne encephalitis virus, p.24938868, 2014. ,
CD8+ T-cells mediate immunopathology in tick-borne encephalitis, Virology, vol.384, 2009. ,
Immunopathology of flavivirus infections, Immunology and Cell Biology, vol.86, issue.1, pp.33-42, 2007. ,
DOI : 10.1038/sj.icb.7100012
TNF-alpha acts as an immunoregulator in the mouse brain by reducing the incidence of severe disease following Japanese encephalitis virus infection, PLoS One, vol.8, p.23940775, 2013. ,
A BHK-21 cell culture-adapted tick-borne encephalitis virus mutant is attenuated for neuroinvasiveness, Vaccine, vol.21, issue.25-26, pp.4043-4051, 2003. ,
DOI : 10.1016/S0264-410X(03)00269-X
Viral Interference. Some Considerations of Basic Mechanisms and Their Potential Relationship to Host Resistance, Bacteriol Rev, vol.24, pp.151-166, 1960. ,
Effects of Defective Interfering Viruses on Virus Replication and Pathogenesis In Vitro and In Vivo, Adv Virus Res, vol.40, pp.181-211, 1991. ,
DOI : 10.1016/S0065-3527(08)60279-1
Characterization of a Siberian Virus Isolated from a Patient with Progressive Chronic Tick-Borne Encephalitis, Journal of Virology, vol.77, issue.1, pp.25-36, 2003. ,
DOI : 10.1128/JVI.77.1.25-36.2003
Attenuation by a Thousand Cuts, New England Journal of Medicine, vol.359, issue.21, pp.2283-2285, 2008. ,
DOI : 10.1056/NEJMcibr0805820
Low-usage codons in Escherichia coli, yeast, fruit fly and primates, Gene, vol.105, issue.1, pp.61-72, 1991. ,
DOI : 10.1016/0378-1119(91)90514-C
Analysis of synonymous codon usage in foot-and-mouth disease virus, Veterinary Research Communications, vol.368, issue.4, pp.393-404, 2010. ,
DOI : 10.1007/s11259-010-9359-4
CodonW v1.3, 1997. ,
RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests, PLoS ONE, vol.45, issue.2, p.21347398, 2011. ,
DOI : 10.1371/journal.pone.0016142.s004
High-Fat Diet: Bacteria Interactions Promote Intestinal Inflammation Which Precedes and Correlates with Obesity and Insulin Resistance in Mouse, PLoS ONE, vol.10, issue.10, p.20808947, 2010. ,
DOI : 10.1371/journal.pone.0012191.t005
A simple method of estimating fifty per cent endpoints, Am J Hyg, vol.27, pp.493-497, 1938. ,