Genetic Variability of Tick-Borne Encephalitis Virus Genome 5′-UTR from Northern Eurasia

This paper reports the analysis of the nucleotide sequences of the 5'-untranslated region (5'-UTR) of tick-borne encephalitis virus (TBEV) genomic RNA isolated from 39 individual taiga ticks collected in several regions of Northern Eurasia. The sequences of 5'-UTRs of the Siberian and Far East TBEV genotypes were 89% and 95% identical to the prototype strains (Zausaev and 205), respectively. The detected nucleotide substitutions were typical for these two TBEV genotypes, which made possible unambiguous identification. Both conservative and variable motifs were detected in the 5'-UTR RNA. The B2, C1, and C2 elements of the Y-shaped 5'-UTR structure and the presumable viral RNA-dependent RNA-polymerase binding site were the most variable. The A2, CS A, CS B elements as well as the start codon were conservative. Interestingly, five substitutions in the 5'-UTR Cl variable element of the TBEVs isolated in different geographical regions were strictly conservative, while 11 different substitutions were detected in this element among the laboratory TBEV variants. A little less that a third of all nucleotide substitutions were mapped outside the main elements of the Y-shaped structure. In general, nucleotide substitutions were localized to stem structures, not being found in the hairpin regions of the TBEV 5'-UTR. The results indicated significant variability of the genomic RNA 5'-UTR in the TBEV laboratory strains and field isolates obtained from different geographical regions. It has been suggested that genetic variability of 5'-UTR is characteristic of the TBEV genome 5'-UTR organization and may serve as a structural basis for virus efficient replication in various avian, mammalian, and ixodic tick cells.

Automated summary

This study analyzed the nucleotide sequences of TBEV genomic RNA isolated from ticks collected in Northern Eurasia, revealing significant variability in the 5'-UTR among different TBEV genotypes. The identified nucleotide substitutions were typical for specific TBEV genotypes and located mainly in stem structures of the 5'-UTR. The findings suggest that genetic variability in the 5'-UTR may play a role in the efficient replication of TBEV in various host cells.