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Origin and distribution of tick-borne encephalitis virus strains of the Siberian subtype in the Middle Urals, the north-west of Russia and the Baltic countries

¹ Laboratory of Molecular Genetics, Department of Biology, Ural State University, Lenin Avenue 51, Yekaterinburg 620083, Russia
² Arbovirus Laboratory, Yekaterinburg Research Institute of Viral Infections, Letnyaya 23, Yekaterinburg 620030, Russia
³ Laboratory of Viral Diseases, FSHI Sverdlovsk Oblast Hygiene and Epidemiology Centre, Otdel'nyi 3, Yekaterinburg 620078, Russia

Correspondence
S. Yu. Kovalev
Sergey.Kovalev{at}usu.ru

Tick-borne encephalitis virus (TBEV) plays an important role in infectious human morbidity, particularly in Russia and the Middle Urals. The Siberian subtype of TBEV (S-TBEV) is dominant in the Middle Urals. Determining the origin of S-TBEV strains in this territory and also in the European part of Russia and the Baltic countries is very important for understanding the cause of its distribution. The surface glycoprotein E gene was partially sequenced in 165 S-TBEV isolates collected in the Middle Urals between 1966 and 2008. Nucleotide and amino acid sequence identity of the studied isolates is 94 and 97.4 %, respectively. Eighty per cent of them are represented by six clusters with identical amino acid sequences in the glycoprotein E fragment analysed. We have determined four types of isolate distribution in the explored territory: local, split, corridor and diffuse. The average rate of nucleotide substitutions per site year^–1 is estimated to be 1.56x10^–4. The age of the S-TBEV population was evaluated to be slightly less than 400 years. Phylogenetic analysis of the data and comparison with historical events indicate that the distribution of S-TBEV strains in the Middle Urals and the European part of Russia originated twice from different foci in western Siberia. This is related to the first land road into Siberia and the Trans-Siberian Way, which functioned at different times. The main reason for such rapid distribution of S-TBEV strains is the anthropogenic factor, i.e. human economic activity during the colonization of new territories in Siberia in the recent past.

A list of TBEV strains and a phylogenetic tree of S-TBEV strains based on gene E fragment sequences are available with the online version of this paper.