A NOVEL METHOD FOR PESTIVIRUS GENOTYPING BASED ON PALINDROMIC NUCLEOTIDE SUBSTITUTIONS IN THE 5'-UNTRANSLATED REGION

A simple and practical method was developed for pestivirus genotyping based on analysis of the secondary structures in the 5'-untranslated r egion (UTR). Three stable stem-loop structures, V1, V2 and V3, predict ed by computer in the 5'-UTR, included strictly conserved consensus ba se-pairings which are shared by all the genotypes of pestivirus or are characteristic to each genotype of pestivirus. On the basis of the pa lindromic nucleotide substitution at the secondary structural level, s ix genotypes have been identified among pestivirus strains, irrespecti ve of the cytopathic and non-cytopathic biotypes. They are genotypes I a, Ib, Ic and II in bovine viral diarrhea virus, genotype III in borde r disease virus, and genotype IV in classical swine fever virus. The s table stem-loop structures, which were maintained by palindromic nucle otide substitutions in the stem region, may represent references for t he classification and identification of pestivirus species and/or geno types. (C) 1998 Elsevier Science B.V, All rights reserved.