Using poliovirus (PV) and its RNA-dependent RNA polymerase (RdRp), 3Dpol, as our primary model system, we, our collaborators and other picorna virologists have made a very compelling case for RdRp fidelity and the corresponding genetic diversity of the viral population as contributors to viral pathogenesis and virulence. This relationship between viral genetic diversity and viral fitness established using the PV model has now been demonstrated for a variety of virus families. In addition, we have demonstrated that the rate of nucleotide addition can be tuned and contributes to viral genetic diversity and viral fitness. Therefore, the overarching hypothesis driving our studies is that mechanisms governing RdRp speed and fidelity can be targeted genetically and chemically for development of attenuated viruses and antiviral agents, respectively. If one is to harness the full therapeutic an prophylactic potential of modulated RdRp function, however, knowledge of the physical mechanism(s) controlling RdRp speed and fidelity is needed. One goal of this application is to test and to exploit a new model for nucleotide selection that we anticipate can be applied to any RdRp. Recombination is a major contributor to viral evolution, leading to the emergence of vaccine-resistant strains and expansion of virus host range. Unfortunately, we lack sufficient knowledge of the molecular mechanism of RNA virus recombination to prevent this process from thwarting vaccine development and long- term efficacy. Therefore, an understanding of recombination is of potentially broad, practical value. For example, detailed knowledge of the mechanism of recombination may establish principles that can be exploited for development of strategies to suppress recombination and/or design of recombination-deficient vaccine strains. A second goal of this application is to create fundamental knowledge on the mechanism of RNA virus recombination using the PV model. During the next funding period, our central objectives will be: (1) Identify active-site determinants of RdRp incorporation fidelity that can be targeted for viral attenuation; (2) Exploit the promiscuity of the RdRp nascent base pair-binding pocket for antiviral therapy; (3) Elucidate a mechanism for template switching/strand transfer by PV RdRp and establish its relevance to RNA recombination by PV in cells. The proposed studies will create important knowledge that should contribute to development of strategies to treat and to prevent RNA viral infections, including those of current concern: Ebola virus, enterovirus D68, and Middle Eastern respiratory syndrome coronavirus.

Public Health Relevance

RNA viruses represent an existing and emerging threat to US public health. The proposed studies will create important knowledge that should contribute to development of strategies to treat and to prevent RNA viral infections, including those of current concern: Ebola virus, enterovirus D68, and Middle Eastern respiratory syndrome coronavirus. Achievement of the goals of the application will provide novel targets and mechanisms for development of vaccines and inhibitors to prevent and to treat infections by RNA viruses.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI045818-20
Application #
9679449
Study Section
Virology - A Study Section (VIRA)
Program Officer
Park, Eun-Chung
Project Start
1999-07-01
Project End
2020-04-30
Budget Start
2019-05-01
Budget End
2020-04-30
Support Year
20
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Pennsylvania State University
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
003403953
City
University Park
State
PA
Country
United States
Zip Code
16802
Fitzsimmons, William J; Woods, Robert J; McCrone, John T et al. (2018) A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus. PLoS Biol 16:e2006459
Gizzi, Anthony S; Grove, Tyler L; Arnold, Jamie J et al. (2018) A naturally occurring antiviral ribonucleotide encoded by the human genome. Nature 558:610-614
Li, Chen; Wang, Haiwei; Yuan, Tiangang et al. (2018) Foot-and-mouth disease virus type O specific mutations determine RNA-dependent RNA polymerase fidelity and virus attenuation. Virology 518:87-94
Dulin, David; Arnold, Jamie J; van Laar, Theo et al. (2017) Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers. Cell Rep 21:1063-1076
Yang, Xiaorong; Liu, Xinran; Musser, Derek M et al. (2017) Triphosphate Reorientation of the Incoming Nucleotide as a Fidelity Checkpoint in Viral RNA-dependent RNA Polymerases. J Biol Chem 292:3810-3826
Li, Sixing; Ma, Fen; Bachman, Hunter et al. (2017) Acoustofluidic bacteria separation. J Micromech Microeng 27:
Li, Sixing; Ren, Liqiang; Huang, Po-Hsun et al. (2016) Acoustofluidic Transfer of Inflammatory Cells from Human Sputum Samples. Anal Chem 88:5655-61
Cameron, C E; Moustafa, I M; Arnold, J J (2016) Fidelity of Nucleotide Incorporation by the RNA-Dependent RNA Polymerase from Poliovirus. Enzymes 39:293-323
Lee, Cheri A; August, Avery; Arnold, Jamie J et al. (2016) Polymerase Mechanism-Based Method of Viral Attenuation. Methods Mol Biol 1349:83-104
Woodman, Andrew; Arnold, Jamie J; Cameron, Craig E et al. (2016) Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination. Nucleic Acids Res 44:6883-95

Showing the most recent 10 out of 50 publications