EV D68 5\u27UTR Structure Analysis via SHAPE-MaP

Enterovirus D68 is a single-stranded positive-sense RNA virus belonging to picornaviridae family. First isolated in 1962 in California, EV-D68 only had minor cases of respiratory illness associated with it until 2014. Since the summer of 2014, reported outbreaks for EV D68 has been increasing with a strong association with polio-like acute flaccid myelitis (AFM). EV D68 utilizes its 5\u27 untranslated region (5\u27UTR) to recruit the ribosome to undergo cap-independent translation. Ample evidence suggests that the 5\u27UTR which includes the internal ribosome entry site (IRES) plays an important role in determining the virulence of the virus. Understanding the structural changes in 5\u27UTR of current EV D68 strains from the ones in 1962 can help determine the reason for its newly gained neurotropism. A robust secondary structure of the 5\u27UTR will be generated using the SHAPE- MaP analysis. This method involves chemical modification of the 2\u27 hydroxyl group of nucleotides in the RNA molecules based on their position and flexibility. The modified molecule is converted into cDNA and sequenced to create mutational profiles. By analyzing the sequence and using computational tools, the 5\u27UTR structure can be generated. Elucidating a novel 5\u27UTR of EV D68 will not only reveal the structural changes leading to neurotropism but comparative studies with other structures will also help find virulence determining key structural features shared among enteroviruses