Baltic lineage of tick-borne encephalitis virus: A putative evolutionary pathway

Tick-borne encephalitis virus (TBEV) is transmitted by ixodid ticks and has three subtypes. The most genetically heterogeneous and widely distributed is the Siberian subtype which is subdivided into two main phylogenetic lineages, Asian (TBEV-Sib^Asia) and Baltic (TBEV-Sib^Baltic). According to the hypothesis of quantum evolution of TBEV (Kovalev et al., 2014b), TBEV-Sib^Asia originated about 370 years ago in Siberia, but the question concerning the time and place of origin of TBEV-Sib^Baltic is still to be solved. In the present paper, the sequences of a gene E fragment of 20 newly obtained TBEV-Sib^Baltic strains and 164 sequences of TBEV-Sib^Baltic from GenBank were analysed. The clusteron approach applied to TBEV-Sib^Baltic allowed the identification of three new clusterons. We revealed three clades of TBEV-Sib^Baltic, each characterized by a certain geographical distribution, and estimated their evolutionary ages. The oldest clade was Balt I, which presumably originated in North-West Russia and the Baltic countries about 300 years ago as a result of human activity, and then gave rise to the other clades in the Urals and West Siberia. The European subtype of TBEV and TBEV-Sib^Baltic may have originated simultaneously from the clusteron-founder 3A of TBEV-Sib^Asia, the former through the adaptation of the virus to Ixodes ricinus, the latter - to a European subpopulation of Ixodes persulcatus. The use of the clusteron approach complemented with the results of phylogenetic analysis, data on the geographical distribution of the virus, the population structure of ticks, and the historical evidence allow us to estimate evolutionary pathways of the subtypes and phylogenetic lineages of TBEV.