Files
Abstract
Wastewater-based epidemiology (WBE) has garnered significant attention as an early warning tool for detecting and predicting the course of COVID-19 cases within a community, working alongside public health data. This monitoring approach has been employed in various settings, including municipal wastewater treatment centers, universities, and community living spaces, to track COVID-19 trends. To effectively conduct WBE surveillance, it's imperative to quantify viral copies precisely and reliably from wastewater. The accuracy of SARS-CoV-2 quantification hinges on the selection of an efficient and dependable virus concentration method. The concentration of samples plays a pivotal role, particularly when the viral load in untreated wastewater falls below the threshold detectable by Reverse Transcriptase Quantitative Polymerase Chain Reaction (RT-qPCR) analysis.The first objective of my dissertation, discussed in Article 1, is the performance evaluation of a rapid ultrafiltration-based virus concentration method using InnovaPrep Concentrating Pipette (CP) Select and how it compares with electronegative membrane filtration (HA) method. The criteria of the evaluation were based on the SARS-CoV-2 detection sensitivity, surrogate virus recovery rate, and sample processing time. Results suggested that the CP Select concentrator was more efficient at concentrating SARS-CoV-2 from wastewater compared to the HA method. About 25% of samples that tested SARS-CoV-2 negative when concentrated with the HA method produced a positive signal with the CP Select protocol. The optimization of the CP Select protocol by adding AVL lysis buffer and sonication increased Bovine Coronavirus (BCoV) recovery by 19%, which compensated for viral loss during centrifugation. Filtration time decreased by approximately 30% when using the CP Select protocol, making this an optimal choice for building surveillance applications where quick turnaround time is necessary. The second objective of my dissertation, discussed in Article 2, aims to develop and optimize a large-volume concentration method for increased sensitivity in detecting SARS-CoV-2, particularly during periods of low COVID-19 infection. Most current virus concentration methods have inherent limitations, as they can only process small volumes of wastewater, typically ranging from 20 to 250 mL. While small-volume methods are effective for detecting and quantifying SARS-CoV-2 during high community infection, they may lack informativeness during the early stages of community infections. In this study, we filtered 3 liters of wastewater through a hollow ultrafilter (UF) and then further concentrated the first eluate using the electronegative membrane filter, also known as the HA filter. The optimized combination method, UF-HA_Soni, resulted in a 100% positive detection rate for SARS-CoV-2 during low COVID-19 infection period. In contrast, the UF and HA methods used individually achieved detection rates of 63% and 9%, respectively. During high COVID-19 infection periods, no significant difference in SARS-CoV-2 detection was observed. However, the hollow UF method yielded a higher mean SARS-CoV-2 concentration. Additionally, the UF method successfully recovered 33.2% of Bovine Coronavirus (BCoV), which was significantly greater than any of the alternative methods. Our analysis of virus partitioning revealed that 26% of SARS-CoV-2 viruses were attached to solid particles, with the majority found in smaller suspended particles separated by centrifugation, as opposed to the larger gravity-settled solids. The third objective of my dissertation as discussed in Article 3 is to evaluate the application of the digital droplet PCR (ddPCR) to detect and quantify SARS-CoV-2 variants in wastewater. We used two mutation assays targeting the S gene (N764K and N856K) to detect and quantify SARS-CoV-2 Omicron and Delta variants. With these two assays, we first detected the Omicron variants on December 6, 2021, in the wastewater sample from Mecklenburg County. This detection preceded the first clinical detection on December 10, 2021. The relative abundance of Omicron VOCs determined by RT-ddPCR in wastewater showed a strong and positive correlation with clinically reported VOCs (r = 0.98, p < 0.0001). This surveillance method for variant analysis provided near real-time insights into the transmission dynamics of Omicron variants, facilitating swift administrative interventions, including awareness, preparedness, and control measures.