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

Abstract

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 C1 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.

Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology

“…The TBEV 5ʹUTR has a canonical length of 132 nt throughout all subtypes. Despite conservation of 5ʹUTR length, there is considerable sequence variability that accounts for average sequence identity levels between 89 and 95 per cent for TBEV-Sib and TBEV-FE, respectively ( Ponomareva et al. 2021 ).…”

Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology

“…The TBEV 5’UTR has a canonical length of 132 nt throughout all subtypes. Despite conservation of 5’UTR length, there is considerable sequence variability that accounts for average sequence identity levels between 89% and 95% for TBEV-Sib and TBEV-FE, respectively [58]. This heterogeneity at the primary sequence level, however, does not translate into structural diversity.…”

The comparative genomic analysis provides insights into the phylogeny and virulence of tick-borne encephalitis virus vaccine strain Senzhang

“…Genome-wide synteny analysis of the Senzhang strain and three reference strains (Neudoerfl strain for European subtype [22], 205 strain for Far-Eastern subtype [23,24], and Vasilchenko strain for Siberian subtype [12,25]) showed that the Senzhang strain had high synteny with the other three subtypes. However, there was significant variation at the 3' end of the genome sequence.…”