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Tick-borne encephalitis is a zoonotic infection of a central nervous system whose clinical course is often severe, even fatal, and complications (such as paralysis) are frequent [Zlobin and Lvov, 2008]. It is caused by tick-borne encephalitis virus (TBEV) belonging to the mammalian tick-borne flaviviruses group in the genus Flavivirus (Flaviviridae). The group includes several species found in geographically distant regions of Eurasia and North America. Evolutionary and genetic relationships among these viruses as well as among TBEV strains proper are not clear, which results in the contradiction of classification schemes suggested by different authors. There is a widely shared opinion that three antigenic TBEV subtypes correspond to three major TBEV genotypes, the Far Eastern (TBEV-FE, with Sofjin strain as a prototype), European (TBEV-Eu, prototype Neudoerfl strain), and Siberian or Ural-Siberian (TBEV-Sib, prototypes Vasilchenko and Zausaev strains) (Fig. 1) [Ecker et al., 1999; Hayasaka et al., 1999, 2001; Zlobin et al., 2001a, 2003; Pogodina et al., 2002, 2004]. In 2001 as a result of studying TBEV genetic variability the existence of six genotypes of the virus was supposed on the basis of homology analysis of a small part of the E gene (160 nt) of 34 strains [Zlobin et al., 2001a,b]. Three of them were accepted as the main ones [Zlobin et al., 2003]. The Turkish strain described earlier as a separate strain in the TBEV virus subgroup [Gao et al., 1993] was included in the genotype 6 together with the strain Vergina [described as a strain of TBEV by Pogodina et al., 1993] and classified as the variant of Louping ill virus (LIV, the Scottish sheep encephalomyelitis virus) [Heinz et al., 2000]. Genotypes 4 and 5 were represented by single strains, 178-79 and 886-84. These strains were isolated in the Irkutsk region and met the criteria for classification into independent genotypes according to the degree of genomic differences [Zlobin et al., 2001a]. Then, the complete genome sequences of 178-79 and 886-84 strains have been determined [Karan’ et al., 2007a,b]. Phylogenetic analysis has revealed that strain 178-79 to the greater degree and

Genetic Studies of Tick-Borne Encephalitis Virus Strains from Western and Eastern Siberia