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Principal Investigator: Mark T Heise
Organization: UNIV OF NORTH CAROLINA CHAPEL HILL
Fiscal Year: 2019
Award: $192,793
Funding agency: National Institute of Allergy and Infectious Diseases
Abstract
Chikungunya virus (CHIKV) is a mosquito borne alphavirus that causes massive outbreaks of severe debilitating
arthritis in humans (1). Despite CHIKV’s status as a significant emerging disease threat, there are currently no
approved vaccines or therapies for CHIKV. Therefore, the development of new vaccines/therapies requires that
we understand how this important human pathogen replicates and causes disease. While most studies of CHIKV
virulence determinants focus on defining the function of viral proteins, there is a growing appreciation of the role
of non-coding RNA structural elements in virus replication and pathogenesis. However, the full range of RNA
secondary structures within the CHIKV genome is not known, nor is it understood how these structures affect
virus biology or disease pathogenesis. We therefore used selective 2′-hydroxyl acylation analyzed by primer
extension and mutational profiling (SHAPE-MaP) to define the RNA structure of the entire CHIKV genome of a
clinical isolate from the ongoing CHIKV epidemic in the Americas. This analysis provided the first comprehensive
analysis of RNA structure in an alphavirus genome. We identified high levels of RNA secondary structure
distributed throughout the genome, including 23 regions with exceptionally high structural stability. Five of these
highly stable structures were previously shown (e.g the 5’ CSE, 26S promoter region) to play important roles in
the CHIKV lifecycle. The remaining 18 novel RNA structures have not previously been characterized. We also
identified three different isoforms of the CHIKV 3’ UTR. Each differed significantly in their RNA secondary
structure, and these differences correlated with their ability to replicate in mosquito cells or cause disease in a
mouse model of CHIKV-induced arthritis. These results demonstrate that the CHIKV genome is highly structured,
and lead us to hypothesize that the novel RNA structures we identified play important roles in multiple aspects
of the CHIKV lifecycle. In Aim 1 we test whether novel, highly stable RNA structures in the CHIKV genome are
important for CHIKV replication and disease pathogenesis. In Aim 2 we define the role of a specific RNA
structural element in the viral 3’ UTR in regulating CHIKV host range and viral virulence. These studies
significantly advance our understanding of how alphavirus RNA structure impacts multiple aspects of CHIKV
biology, and provide new insights that can be used to develop safer and more effective CHIKV vaccines and
therapies.
Terms: <3' Untranslated Regions><3'UTR><Acute><Acylation><Affect><Alpha Virus><Alphavirus><Americas><Anti-Viral Response><Antiviral Agents><Antiviral Drugs><Antiviral Response><Antivirals><Arthritis><Attenuated Live Virus Vaccine><Biology><CHIKV><Caribbean><Caribbean Sea Region><Caribbean region><Cell Body><Cells><Chikungunya virus><Clinical><Code><Coding System><Complex><Country><Culicidae><DNA Molecular Biology><Data><Development><Disease><Disease Outbreaks><Disorder><Elements><Epidemic><Functional RNA><General Viruses><Genetic Alteration><Genetic Change><Genetic Translation><Genetic defect><Genome><Group A Arboviruses><Human><Hydroxyl><Hydroxyl Radical><Indian Ocean><Insect Vectors><Isoforms><Knowledge><Lead><Length><Life Cycle><Life Cycle Stages><Live-attenuated Vaccine><Mammalia><Mammals><Measures><Messenger RNA><Modern Man><Molecular Biology><Mosquitoes><Mutation><Non-Coding><Non-Coding RNA><Non-Polyadenylated RNA><Non-translated RNA><Noncoding RNA><Nontranslated RNA><Nucleotides><Outbreaks><Pathogenesis><Pb element><Play><Primer Extension><Promoter Regions><Promotor Regions><Protein Isoforms><RNA><RNA Gene Products><RNA analysis><Research><Resolution><Ribonucleic Acid><Role><Southeast Asia><Southeastern Asia><Structure><Testing><Therapeutic><Time><Tropism><Untranslated RNA><Vaccines><Validation><Variant><Variation><Viral><Viral Activity><Viral Diseases><Viral Function><Viral Gene Products><Viral Gene Proteins><Viral Genome><Viral Pathogenesis><Viral Physiology><Viral Proteins><Virulence><Virus><Virus Diseases><Virus Replication><West Indies Region><anti-viral agents><anti-viral drugs><anti-virals><arthritic><computer program><computer programming><developmental><genetic promoter element><genome mutation><heavy metal Pb><heavy metal lead><human disease><human pathogen><in vivo><insight><life course><mRNA><mRNA Translation><mosquito-borne><mosquitoborne><mouse model><murine model><mutant><new vaccines><next generation vaccines><noncoding><novel><novel vaccines><nuclease><pathogen><social role><stem><viral RNA><viral infection><viral multiplication><viral replication><virus RNA><virus genome><virus infection><virus multiplication><virus pathogenesis><virus protein><virus-induced disease>