Insights into biomolecular reactivity and structure for virus inactivation prediction

The emergence and spread of new viruses such as SARS-CoV-2 and its variants has heightened the need to assess the efficacy of virus inactivation by disinfectants including chemical oxidants such as chlorine and chlorine dioxide. Culture-based approaches are the current gold standard methods to track the levels of infective viruses before and after disinfection. However, many viruses are not culturable, or are too dangerous to be cultured, and thus their mechanisms of inactivation by chemical oxidants are not well understood. The overarching goal of this project is to investigate and unravel the fundamental reactions and structural changes of viral proteins that occur during virus inactivation by chemical oxidants such as chlorine and chlorine dioxide. To advance this goal, the Principal Investigator (PI) propose to integrate high-throughput and high-sensitivity proteomic analysis, structural analysis, and data mining to test the hypothesis that virus inactivation by oxidants is driven by the decay of viral proteins, and the decay rate constants of viral peptides is a function of solvent accessibility of susceptible amino acid residues in the peptide sequences. The successful completion of this project will benefit society through the development of a mechanistic understanding of virus susceptibility to disinfectants that could provide guidance to the public and water utilities regarding the selection of the most efficient chemical oxidants and disinfectant dosages to inactivate waterborne viruses while minimizing the formation of toxic disinfection byproducts. Additional benefits to society will be achieved through student education and training including the mentoring of a graduate student at the University at Buffalo. A virus particle consists of a single molecule of genome, which is surrounded by a protein capsid, and/or lipid envelope. The viral genome and proteins carry various biological functions that are essential for virus infection. Previous studies of virus inactivation by UV and chemical oxidants suggest that the degradation of viral biomacromolecules, particularly the genome and proteins, correspond to the loss of virus infectivity. However, a fundamental understanding of the mechanisms of virus inactivation by chemical oxidants has remained elusive. To address this critical knowledge gap, the Principal Investigator (PI) of this project proposes to integrate high-throughput and high-sensitivity proteomic analysis, structural analysis, and data mining to investigate and unravel the mechanisms of oxidation of viral proteins by chemical disinfectants. The specific objectives of the research are to: (1) Characterize viral protein degradation by chemical oxidants and identify structural features of viral peptides that drive virus inactivation using chlorine and chlorine dioxide as model disinfectants; (2) Evaluate the impacts of oxidative modifications and peptide cleavages on the conformational change of viral proteins; and (3) Evaluate the impacts of lipid permeability to oxidant molecules on the extents and rates of inactivation of enveloped waterborne viruses. The successful completion of this research has the potential for transformative impact through the development and validation of a new model that could predict the decay kinetics of viral proteins when viruses are treated by oxidants and help identify the biomolecular features of viral proteins that control virus susceptibility or resistance to disinfectants. To implement the education and outreach activities of the project, the PI plans to incorporate the findings from this research into undergraduate and graduate courses at the University at Buffalo (UB). In addition, the PI proposes to leverage the UB Louis Stokes Alliance for Minority Participation (LSAMP) Summer Research Internship Program to recruit two undergraduate students from underrepresented groups that will work on the project. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.