Predicted stem-loop structures and variation in nucleotide sequence of 3' noncoding regions among animal calicivirus genomes.
Caliciviruses are nonenveloped with a polyadenylated genome of approximately 7.6 kb and a single capsid protein. The "RNA Fold" computer program was used to analyze 3'-terminal noncoding sequences of five feline calicivirus (FCV), rabbit hemorrhagic disease virus (RHDV), and two San Miguel sea lion virus (SMSV) isolates. The FCV 3'-terminal sequences are 40-46 nucleotides in length and 72-91% similar. The FCV sequences were predicted to contain two possible duplex structures and one stem-loop structure with free energies of -2.1 to -18.2 kcal/mole. The RHDV genomic 3'-terminal RNA sequences are 54 nucleotides in length and share 49% sequence similarity to homologous regions of the FCV genome. The RHDV sequence was predicted to form two duplex structures in the 3'-terminal noncoding region with a single stem-loop structure, resembling that of FCV. In contrast, the SMSV 1 and 4 genomic 3'-terminal noncoding sequences were 185 and 182 nucleotides in length, respectively. Ten possible duplex structures were predicted with an average structural free energy of -35 kcal/mole. Sequence similarity between the two SMSV isolates was 75%. Furthermore, extensive cloverleaflike structures are predicted in the 3' noncoding region of the SMSV genome, in contrast to the predicted single stem-loop structures of FCV or RHDV.
Virology Swine Research Unit, National Animal Disease Center, USDA, Ames, IA.
B S
BS
Seal
J D
JD
Neill
J F
JF
Ridpath
D001483:Base Sequence; D002139:Caliciviridae / Q000235:genetics*; D017927:Calicivirus, Feline / Q000235:genetics; D003198:Computer Simulation; D017124:Conserved Sequence; D004274:DNA, Recombinant; D016679:Genome, Viral; D017929:Hemorrhagic Disease Virus, Rabbit / Q000235:genetics; D007438:Introns; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012330:RNA, Double-Stranded / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid
D004274:DNA, Recombinant; D012330:RNA, Double-Stranded; D012367:RNA, Viral