The genomes of RNA viruses often contain RNA structures that are crucial for translation and RNA replication and may play additional, uncharacterized roles during the viral replication cycle. RNA structure with single-nucleotide resolution. In combination with orthogonal evolutionary analyses, we uncover several conserved RNA structures in the open reading frame of the viral genome. The genomes of RNA viruses, such as poliovirus (PV), often contain complex RNA secondary and tertiary structures.
These structures are crucial for translation and replication of the viral genome and may play additional roles in other processes, such as genome packaging and modulation of the host antiviral response. We have used SHAPE to interrogate authentic full-length poliovirus genomic RNA extracted, in a gentle and non-denaturing manner, from purified virions. We identified many regions of the poliovirus genome where SHAPE data indicate that nucleotide flexibility is constrained, suggesting that the RNA is folded into secondary and/or tertiary structures. We then complemented our chemical probing with a parallel, independent evolutionary analysis of pairing probability, which demonstrated that several of the newly identified structures are also highly conserved.