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Molecular typing revealed mono- or mixed infection with three main subtypes of TBEV in ticks and small mammals. The Siberian subtype was more common in ixodid ticks, and the FE subtype was more common in small mammals (p < 0.001). TBEV isolates of the European subtype were rare. TBEV infection among different species of small mammals did not correlate with their infestation rate with ticks in the Novosibirsk region, Russia.

With the use of the ELISA method to detect an antigen, reverse transcription with quantitative real-time PCR with subtype-specific fluorescent probes, phylogenetic analysis of E and NS1 gene nucleotide sequences, bioassays with suckling mice, hemagglutination and neuroinvasiveness tests there was made a comparison of the tick-borne encephalitis virus (TBEV) infection of ixodid ticks Ixodes persulcatus P.Schulze and Ixodes pavlovskyi Pomerantsev 1946 in the area of sympatria of their natural habitats in the Novosibirsk region during growth period of their populations with the replacement ofprevailing species of monodominant type of the ixodid population structure. The ratio of 2 tick species didn’t depend on biotopes ofpine or birch forest but rather on the distance from the Novosibirsk Scientific Center: the lower anthropogenic pressure the smaller I.pavlovskyi proportion. The TBEV rate (including both pathogenic and apathogenic for laboratory mice virus), spectra of the TBEV3 main genetic types, neurovirulence and hemagglutination activity were similarfor both I.persulcatus and I.pavlovskyi. However, the proportion ofpathogenic for laboratory mice virus and the TBEV Far Eastern subtype, as well as viral loads of Siberian and European types for the TBEV from I.pavlovskyi were significantly higher than those from I.persulcatus.

A comparative analysis of the virus infection carrier state and distribution of genetic types of the virus of tick-borne encephalitis (TBE) among invertebrates (2 species of ticks, Ixodes persulcatus Schulze and Ixodes pavlovskyi Pomerantsev 1946) and vertebrate reservoir hosts (4 species of small rodents: the red vole Myodes rutilus Pallas, gray-sided vole Myodes rufocanus Sundevall, field mouse Apodemus agrarius Pallas, birch mice Sicista betulina Pallas and 1 species of insectivores - common shrew Sorex araneus L (1758)), dominating on the territory of the Novosibirsk region in 2009-14 years, was performed with the use of virological and molecular biological methods. Frequency detection of RNA and / or E protein in mammals (70,9 ± 3,0%) were shown to considerably exceed levels of virus infection carrier state rate of ticks (3,4 ± 0,4). In the circulation of three major types of TBE - Far East (FE), Siberian (NIB) and European (Eur) in natural populations in mono - or polytype forms in mites Sib type prevailed (p