Hepatitis C virus (HCV) infects a large population within the United States (~2%), where it remains a major cause of chronic liver disease and cancer. While potent antiviral drugs have recently become available, long-term success in combating HCV-related disease requires a clear understanding of viral replication mechanisms. Furthermore, HCV provides an essential model system for understanding the replication of many related positive-strand RNA viruses, including dengue virus and other unmet threats to human and animal health. To date, most work on HCV replication has focused on activities of the viral nonstructural (NS) proteins or the role of host factors in this process. Very little has been done on role of the HCV RNA genome in replication or on the functional interactions between the viral genome and NS proteins. This is a critical gap, since the interaction between HCV RNA and viral proteins is literally where the ?rubber hits the road?, and the key events in viral replication occur. We will leverage our recent success in defining molecular networks among the NS proteins, and in characterizing RNA and RNA-protein complexes, and we will exploit new approaches for monitoring RNA interactions in vivo in order to achieve the following three aims: (A) Determine the functional RNA structures within the HCV genome; (B) Define the molecular interactions between NS proteins and the RNA genome, establishing their interaction sites and functional relevance during sequential phases of the viral lifecycle; (C) Define the structural features and functional attributes of the Replication Pre-initiation Complexes (RPIC), which initiates the entire process of virus propagation. These objectives will be accomplished by integrating innovative approaches for studying viral genetics, RNA crosslinking and sequencing, enzymology and crystallography, and capitalizing on our respective strengths in virology and RNA biochemistry. By focusing on the molecular interplay between genomic RNA and NS proteins, the work is conceptually innovative. In developing the tools needed to advance this research, the project is also technologically innovative, resulting in methods and reagents that will be of widespread utility to the RNA virus research community.

Public Health Relevance

We are elucidating the structure and mechanism of the machinery that drives replication of hepatitis C virus (HCV). HCV and related viruses represent major threats to public health, and an understanding of their molecular behavior will facilitate the design of new or improved therapeutic strategies. HCV is now an important model system for guiding research on all RNA viruses, thereby providing insights into strategies for defense against new and emerging infections.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Koshy, Rajen
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Yale University
Schools of Arts and Sciences
New Haven
United States
Zip Code