Sequence of the structural proteins of tick-borne encephalitis virus (Western subtype) and comparative analysis with other flaviviruses

Abstract

Tick-borne encephalitis (TBE) virus (Western subtype strain Neudoerfl) was cloned and the sequence of 2450 nucleotides of the 5′-terminal region of the genome was determined. By amino acid sequencing and sequence comparisons with other flaviviruses the amino-termini of the structural proteins and protein NS1 were localized. Sequence homologies with other flaviviruses were determined and corresponded well to the established serological classification system of the Flavivirus family. N-Glycosylation sites were found to be conserved to a large extent among members of the same serological subgroup, but not between members of different subgroups. Hydrophilicity plots and sequence comparisons revealed that the TBE virus capsid protein exhibited features distinct from all other flaviviruses. Additionally, the capsid protein coding region of another natural isolate of TBE virus (strain ZZ-9) was sequenced in order to analyze why the capsid protein of this strain exhibited a significantly faster migration rate on SDS-polyacrylamide gels than other TBE virus strains.