Predicted stem-loop structures and variation in nucleotide sequence of 3′ noncoding regions among animal calicivirus genomes

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Abstract
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.

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