Structured RNA markers for genotyping of tick-borne encephalitis virus

Tick-borne encephalitis is one of the most dangerous natural focal infections. The causative agent of the disease is tick-borne encephalitis virus (TBEV ) transmitted by ticks . There are three main subtypes of TBEV with different clinical manifestations of the disease, but existence of other subtypes is also possible. Effectiveness of the disease treatment can largely depend on the correct identification of TBEV genotype. Comprehensive information about the genotype is contained in the full coding sequence of TBEV genome. А limited number of genotyping markers can be extracted from it in the form of relatively short structured RNA fragments. In this paper, a rather general approach to the isolation of structured RNA markers for the genotyping of TBEV is formulated. Three types of structures are considered: periodicity, fractal-like constructs and compactly localized combinations of different types of repetitions. The choice of these structures for the purposes of genotyping and their possible role in the formation of the pathogenic potential of the virus is substantiated. The approach was tested on the full coding sequences of TBEV (161 strains). Examples of the most characteristic markers of each of the three types are given.