Sukhorukov et al.
The Baikal subtype of tick-borne encephalitis virus is evident of recombination between Siberian and Far-Eastern subtypes
PLoS Negl Trop Dis. 2023;17(3):e0011141. doi:10.1371/journal.pntd.0011141

Within Russia, the main subtypes of TBE virus circulating are the European, the Siberian, and the Far Eastern subtypes. Moreover, additional novel distinct groups of variants have been discovered, among which is the Baikal subtype. Variants of the Baikal subtype have been isolated from Ixodes persulcatus ticks and small animals for about 30 years in regions where variants of the Siberian and the Far Eastern subtypes are also present. The Baikal subtype shows a high serological cross-reactivity with the Siberian and Far Eastern subtype.

Phylogenetic analyses have been carried out, especially by use of newly developed Grouping Scan analysis (GS)-based methods to support the hypothesis that the Baikal subtype may have originated by recombination events.

Based on 11 samples of the Baikal subtype of TBE virus, the authors concluded that homologous recombination events between the Siberian and Far Eastern subtype is likely to be the origin of this subtype, where both the Siberian and the Far Eastern subtype circulate (Buryat Republic, Irkutsk and Trans-Baikal regions). It was suggested that additional more recent recombination events happened between the ancestor of the Baikal subtype and Far Eastern subtype. There are variants of the Baikal subtype which have genetic parts being more closely related to the Siberian subtype, while others relate more to the Far Eastern subtype.

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