COMPLETE SEQUENCE OF 2 TICK-BORNE FLAVIVIRUSES ISOLATED FROM SIBERIA AND THE UK - ANALYSIS AND SIGNIFICANCE OF THE 5'-UTR AND 3'-UTR

The complete nucleotide sequence of two tick-transmitted flaviviruses, Vasilchenko (Vs) from Siberia and louping ill (LI) from the UK, have been determined. The genomes were respectively, 10928 and 10871 nucleo tides (nt) in length. The coding strategy and functional protein seque nce motifs of tick-borne flaviviruses are presented in both Vs and LI viruses. The phylogenies based on maximum likelihood, maximum parsimon y and distance analysis of the polyproteins, identified Vs virus as a member of the tick-borne encephalitis virus subgroup within the tick-b orne serocomplex, genus Flavivirus, family Flaviviridae. Comparative a lignment of the 3'-untranslated regions revealed deletions of differen t lengths essentially at the same position downstream of the stop codo n for all tick-borne viruses. Two direct 27 nucleotide repeats at the 3'-end were found only for Vs and LI virus. Immediately following the deletions a region of 332-334 nt with relatively conserved primary str ucture (67-94% identity) was observed at the 3'-non-coding end of the virus genome. Pairwise comparisons of the nucleotide sequence data rev ealed similar levels of variation between the coding region, and the 5 ' and 3'-termini of the genome, implying an equivalent strong selectiv e control for translated and untranslated regions. Indeed the predicte d folding of the 5' and 3'-untranslated regions revealed patterns of s tem and loop structures conserved for all tick-borne flaviviruses sugg esting a purifying selection for preservation of essential RNA seconda ry structures which could be involved in translational control and rep lication. The possible implications of these findings are discussed. ( C) 1997 Elsevier Science B.V.