Development of genomic surveillance and disinfection technologies to control virus transmission in the environment
Advisor: Professor Thanh H. Nguyen
Zoom meeting ID: 898 9379 6189, Password: 918125
Human viral pathogens have a significant impact on public health. Infected individuals, whether humans or animals, release viruses into the environment through their excreta. Many enteric or respiratory viruses can survive and spread through the environment, potentially infecting hosts through contaminated water, food, air, and surfaces of objects. To protect public health from the viruses spreading through the environment, it is necessary that a clear understanding of the transport and fate of viruses in environmental and engineered settings and the design of effective virus disinfection technologies to reduce the risk of infections. However, viruses are tiny, acellular entities with no biological activities and are easy to mutate, leading to dramatic changes in their phenotype. All of these unique features differentiate viruses from other types of pathogens such as bacteria, fungi, protozoa, and worms. Due to these innate characteristics, the current environmental technologies for viruses are neither accurate nor accessible, resulting in a lack of understanding about the virus distribution in the environment and virus inactivation mechanisms. This dissertation proposes genomic surveillance and disinfection technologies to control virus transmission in the environment, ultimately contributing to public health improvement.
Wastewater-based epidemiology (WBE) is an emerging application of environmental surveillance systems to monitor community-wide disease prevalence. I applied WBE to different sizes of sewersheds, including city- and neighborhood-scale sewersheds, and monitored SARS-CoV-2 RNA in wastewater for 17 months. I found that the sensitivity of WBE in virus detection improves by decreasing the sewershed size. However, monitoring small-sized sewersheds requires increases in the number of monitoring sites to cover the surveillance area. Therefore, this dissertation also aims to enhance the accessibility and accuracy of an environmental surveillance system, which mainly consists of three steps: sample processing, target sequence determination, and target sequence detection. First, I developed porcine gastric mucin conjugated magnetic beads (PGM-MBs) and proved the PGM-MBs can effectively concentrate multiple viral species from wastewater. Second, I wrote computer codes and developed a pipeline allowing us to find specific PCR-based assays for SARS-CoV-2 variants or sensitive assays for genetically diverse noroviruses. Third, I developed RT-LAMP-PfAgo assay to monitor viruses in the environment. I confirmed the RT-LAMP-PfAgo assay is a multiplexable and variant-specific assay that can substitute for the RT-qPCR assay in environmental surveillance systems.
Disinfection technology is another important approach to protecting public health and the economy from viral pathogens. There is no such thing as single perfect disinfection technology, rather the optimal technology should be determined based on each technology’s advantages and drawbacks. Thus, it is important to develop novel technologies to have an ample portfolio of disinfection technologies. Diverse types of disinfection technologies have been developed, but a thorough understanding of virus inactivation efficacy, kinetics, and mechanism, which are fundamental information to design the disinfection process for engineering purposes, are challenging to be understood. I developed molecular assays that evaluate the structural integrity, including genome, capsid protein, and receptor-binding protein as well as aggregation, of diverse viral species. Comparisons between the structural changes by these molecular assays and infectious virus titer by plaque assay enable us to reveal viral inactivation mechanisms of disinfection technologies. For example, this dissertation elaborates virus inactivation mechanism by microplasma UV lamp generating monochromatic wavelength at 222 nm, polyphenols in grape seed extracts, proteins in Moringa oleifera seed extracts, and dry heat.
