Conserved RNA Secondary Structures in Picornaviridae Genomes

The family Picornaviridae contains important pathogens including, for example, Hepatitis A virus and Foot-and-Mouth Disease Virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200 to 8500nts. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an IRES region toward the 5'end. <p> This contribution provides a comprehensive computational survey of the complete genomic RNAs and a detailed comparative analysis of the conserved structural elements in seven of the currently nine genera in the family Picornaviridae. Compared with previous studies we find: (1) that only smaller sections of the IRES region than previously reported are conserved at single-base-pair resolution, and (2) that there is a number of significant structural elements in the coding region. Furthermore we identify potential CREs in four genera where this feature has not been reported so far.