5' AND 3' UNTRANSLATED REGIONS OF PESTIVIRUS GENOME - PRIMARY AND SECONDARY STRUCTURE ANALYSES

Within the conserved 5' untranslated region (UTR) of the pestivirus ge nome three highly variable regions were identified. Preceding the poly protein start codon, multiple cryptic AUG codons and several small ope n reading frames are characteristic for all the five pestiviruses. Ins pection of the context of AUGs revealed that the polyprotein initiatio n AUG of pestivirus has a weak context for efficient translation initi ation. The most favorable context was found in two of the cryptic AUGs . Two oligopyrimidine-rich tracts upstream to the conserved either cry ptic or authentic AUG in the 5'-UTR of pestivirus were identified and 83.3% of their nucleotide sequences are complementary to the consensus sequence at the 3' terminus of eucaryotic 18S rRNA. A secondary struc ture model for the 5'-UTR of pestivirus was predicted. Nucleotide sequ ence comparison among five pestiviruses led to the identification of a variable region and a conserved region in the 3'-UTR. A deletion of 4 1 nucleotides was found within the variable region in Osloss. A second ary structure model for the 3'-UTR was also predicted. The structural similarity of the 5'-UTR between pestiviruses and picornaviruses and h epatitis C viruses was demonstrated and the possible implications of f eatures of the 5' and 3'-UTR of pestiviruses are discussed.