title: Genetic variation in vivo and proposed functional domains of the 5' noncoding region of poliovirus RNA.
abstract: Poliovirus has a single-stranded RNA genome of about 7,440 nucleotides (nt) with an unusually long 750-nt noncoding region in the 5' end (5'NCR). Several regulatory functions have been assigned to the 5'NCR. We sequenced the 5'NCRs of 33 wild-type 3 poliovirus strains to study the range and distribution of naturally occurring sequence variations. In this regard, the 5'NCR can be divided into a conserved part (nt 1 to 650) and a hypervariable part (nt 651 to 750). In the conserved part, altogether 234 unevenly distributed nucleotide positions (36%) showed variation. When these positions were plotted against the predicted secondary-structure models, it was found that the existence of most of the proposed stem-loop structures was supported by extensive structure-conserving substitutions in the stems. Regions with conserved sequences, as well as mutational hot spots, were observed. The hypervariable part of the 5'NCR varied up to 56% between the strains studied. The A + U percentage was significantly higher than in the conserved part. The number of AUG codons varied between 5 and 15 in the conserved part of the 5'NCR, while none was found in the hypervariable part. These results provide information that can be used in site-directed mutagenesis and other approaches targeted to reveal the functional domains of the 5'NCR.
authors.affiliation: Department of Virology, National Public Health Institute, Helsinki, Finland.
authors.forename: T
authors.initials: T
authors.lastname: Pöyry
authors.forename: L
authors.initials: L
authors.lastname: Kinnunen
authors.forename: T
authors.initials: T
authors.lastname: Hovi
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D003062:Codon; D014644:Genetic Variation; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016296:Mutagenesis; D009690:Nucleic Acid Conformation; D017955:Poliovirus / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*
chemical_list: D003062:Codon; D012367:RNA, Viral