Research Projects

Japanese encephalitis virus (JEV) is a major cause of neuroinvasive viral encephalitis, affecting billions of people, primarily children under 15, in Southeast Asia and the Western Pacific. Belonging to the Flaviviridae family, JEV is transmitted by Culex mosquitoes. While most infections result in mild symptoms, including fever, headache, and vomiting, severe cases can rapidly escalate to high fever, coma, seizures, paralysis, and even death. The likelihood of fatality increases with the severity of infection, and survivors often experience lasting cognitive and behavioral impairments, along with neurological issues such as speech, hearing, and communication difficulties. The transmission of JEV across the placenta adds complexity to the infection. JEV has a ~11 kb positive strand RNA genome that encodes several structural and non-structural proteins critical to its pathogenicity. Among these, NS1’—a 52-amino-acid C-terminal extension of NS1—is produced during the late phase of infection through programmed ribosomal frameshifting (PRF). NS1’ is instrumental in JEV’s neuroinvasion by crossing the blood-brain barrier and aiding immune evasion by inhibiting IFN-ß production. PRF allows the ribosome to shift reading frames, translating an alternate protein from the same RNA sequence. This shift is regulated by frameshifting elements (FSEs), specific RNA sequences that include a slippery sequence with ZZZNNNH motif (where Z is any three identical nucleotides, N is U or A, and H is A, C, or U). The slippery sequence, linked to a downstream RNA structure, causes ribosomal slippage, leading to a translational pause and a shift in the reading frame. Preliminary analysis of FSEs across various JEV strains reveals a range of conformational ensembles. However, the precise topologies of these FSEs and their impact on JEV PRF remain unknown. Studies on SARS-CoV-2 FSEs highlight the role of conformational flexibility in driving PRF. I propose that the distinct FSE conformations in JEV strains will have differential effects on PRF, contributing to strain-specific outcomes. To test this, I will develop a series of FSE constructs and employ chemical probing to identify the various topologies that JEV FSEs can adopt. This approach will facilitate the generation of single-topology locked FSE variants, offering detailed insights into the PRF mechanism in JEV and its influence on disease progression. This study seeks to advance our understanding of viral RNA FSE conformational dynamics, which co-transcribe and co-translate viral proteins in host cells, thereby promoting virulence and infectivity. These insights will inform the development of strain-specific antiviral strategies that target JEV FSE regions, enhancing current therapeutic approaches beyond the limited point-of-care options available for infected individuals. Given JEV’s serious impact on public health, research into its molecular mechanisms could identify new targets to reduce or prevent disease.