5’UTR STRUCTURAL ANALYSIS OF ENTEROVIRUS D68

Enterovirus D68 is a single-stranded positive-sense RNA virus of the picornaviridae family that utilizes its 5\u27 untranslated region (5\u27UTR) to recruit ribosomes and undergo cap-independent translation. First isolated in 1962 in California, EV-D68 had been reported for minor cases of respiratory illness until 2014. Since the summer of 2014, reported outbreaks for EV D68 have been increasing with a strong association with polio-like acute flaccid myelitis (AFM). Ample evidence suggests that the 750 nucleotides long 5\u27UTR of enteroviruses includes the internal ribosome entry site (IRES) which plays an important role in determining their virulence. Neurotropic strains of EV-D68 have an approximate 20 nucleotide deletion in the spacer region of their 5’UTR. 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. In the lab, an RNA modification strategy called SHAPE-MaP is employed to generate a robust secondary structure 5\u27UTR structure of EV D68. This method involves chemical modification of the 2\u27 hydroxyl group of nucleotides in the RNA molecules based on their position and flexibility. These modified molecules are converted into cDNA to create high-quality mutational profiles (MaP), which are then subjected to massively parallel sequencing. By using computational tools to analyze the mutational profile, a secondary structure of the 5\u27UTR can be generated. Elucidating novel 5\u27UTR secondary structures of EV D68- Fermon (1962) and EV D68- KT347251.2 (2014) strains can reveal the structural changes leading to neurotropism. These novel structures of non-coding RNAs of EVD68 can also be utilized for comparative studies of 5’UTRs between other neurotropic enteroviruses like EV 71- KF312457.1 (1998), Polio Virus, and non-neurotropic enteroviruses like CVB3 to find key shared structures involved in determining the virulence of enteroviruses