Unique signature amino acid substitution in Baltic tick-borne encephalitis virus (TBEV) strains within the Siberian TBEV subtype

Tick-borne encephalitis virus (TBEV) is an arthropod-borne virus, which is transmitted to vertebrates by the bite of infected ticks. TBEV plays an important role in human morbidity in Europe and in Estonia in particular. All three known TBEV subtypes, Western (W-TBEV), Far-Eastern (FE-TBEV), and Siberian (S-TBEV), co-circulate in Estonia. In the present study, we collected ticks in the eastern part of the country where one of the TBEV vectors, Ixodes persulcatus, is prevalent. In total, 8 TBEV strains were isolated and characterized by partial sequencing of the surface E glycoprotein gene. Phylogenetic analysis showed that all 8 strains belonged to the S-TBEV subtype and clustered geographically with Baltic TBEV strains from Estonia, Latvia, and Finland. Analysis of amino acid sequences revealed a new signature amino acid, Asn, at position 175 for Baltic strains from Estonia, Latvia, Finland, and the European part of Russia, and Ala at position 313 for Siberian strains from Novosibirsk, Tomsk, and Irkutsk within the S-TBEV subtype. According to these findings, discrimination of Baltic and Siberian lineages within the S-TBEV subtype is possible. These data support geographic clustering of Baltic TBEV strains within the S-TBEV subtype in contrast to the previous postulation that TBEV strains could not be distinguished according to place and time of isolation. Both signature amino acids, 175 and 313, are located close to each other at one side of the E protein dimer molecule. Protein structure modeling showed that at position 175, the Baltic strains of S-TBEV had lost one hydrogen bond with Asp181, thus making the nearby 177–179 loop more flexible at the molecule surface. At position 313, the Siberian strains of S-TBEV had a substitution of non-polar Thr to polar Ala. Geometrical analysis of the molecular surface around amino acid 313 hinted at the presence of a cleft between this residue and a loop formed by residues 308–311, which has been suggested as a putative flavivirus receptor-binding site. This substitution may influence the binding properties of the cleft formed by signature amino acid 313 and the receptor-binding loop.