A novel method for pestivirus genotyping based on palindromic nucleotide substitutions in the 5′-untranslated region

Genetic Variety of Bovine viral diarrhea virus 2 Strains Isolated from Sheep

“…Thus stable nucleotide variations at this level assume high importance in terms of virus evolutionary history. Nucleotide sequences at the three variable loci, V1, V2 and V3, in the 5'-UTR of pestiviruses have been shown to be palindromic and capable of forming a stable stem-loop structure peculiar to each Pestivirus species [11]. Nucleotide substitutions in the stem regions always occur to maintain the palindromic sequence and thereby form a stable stem-loop structure.…”

“…Thus, this type of mutation is referred to palindromic nucleotide substitutions (PNS). Based on the above mentioned considerations, the observation of nucleotide variations among virus strains at the level of the three specific palindromes in the 5'-UTR has been conceived as method for genotyping [11]. The results of the PNS method are essentially qualitative and provide the exact species classification of an isolate, although they offer no percentage values for homology among species and genotypes.…”

Species characterization in the genus Pestivirus according to palindromic nucleotide substitutions in the 5′-untranslated region

“…Nucleotide sequences at the variable loci, V1, V2 and V3, in the 5´-UTR of pestiviruses have been shown to be capable of forming a stable stem-loop structure peculiar to each Pestivirus species. The observation of nucleotide variations among virus strains at the level of the three specific variable loci in the secondary structure of the 5'-UTR has been conceived as a simple and practical procedure for genotyping (Harasawa and Giangaspero, 1998). The palindromic nucleotide substitutions (PNS) genotyping method has been further improved from the original concept limited to qualitative analysis (Giangaspero and Harasawa, 2007), allowing the taxonomical segregation of the genus Pestivirus into six species: BVDV-1, BVDV-2, CSFV, BDV, the tentative species Giraffe and a new proposed taxon named Pronghorn.…”

“…The minimum free energy was calculated by the method of Freier et al (1986). Relevant secondary structure regions in the 5'-UTR were used for genotyping based on the palindromic nucleotide substitutions method (Harasawa and Giangaspero, 1998;Giangaspero and Harasawa, 2007). The identification of species within the genus has been achieved according to highly conserved base pairs in the three variable palindromic loci, based on a series of specific passages focused on the qualitative and quantitative analysis of the secondary structures of the strains in the genus.…”

Genotypic Characteristics of Bovine Viral Diarrhea Virus 2 Strains Isolated in Northern Italy.

“…Folding energies of the secondary structures were calculated by the method of Freier et al [3]. Genotyping was performed according to the method described by Harasawa and Giangaspero [9]. Relevant variations in the three variable loci, V1, V2 and V3, characteristic stem-loop palindromic sequences, at the 5'-UTR were considered for the phylogenetic analysis.…”