Methods Development for SARS-CoV-2 Wastewater Surveillance

Wastewater surveillance has proven to be a useful tool to monitor pathogens such as SARS-CoV-2. Wastewater testing is a nonintrusive way to survey the whole population contributing to a sewershed and monitor COVID-19 levels over time. As the pandemic progressed, laboratory methods to process wastewater and quantify SARS-CoV-2 RNA levels transitioned and improved as technologies changed, projects expanded sample numbers, and supply chain issues resolved. Maintaining data continuity is crucial for labs undergoing a method transition so they are able to accurately assess COVID-19 levels over time and compare RNA detection values to public health data. Chapter I of this thesis describes an RNA extraction kit comparison project that was done to compare ThermoFisher, Promega and Macherey-Nagel RNA extraction kits. To evaluate the kits, we looked at their sensitivity, variability and efficiency and saw that the ThermoFisher RNA extraction kit was the best overall. In Chapter II of this thesis, a lab transition is described from a low-throughput manual filtration-based wastewater concentration and RNA extraction followed by qPCR to a high-throughput automated magnetic bead-based concentration and extraction followed by dPCR. During the two-month transition period, wastewater samples from across the Chicagoland area were processed with both methods in parallel. We evaluated a variety of models to relate the RNA measurements from both methods and found that a Log-Log model was most appropriate to relate the datasets after removing outliers and inconsistent points to improve model performance. This study demonstrates that data continuity can be maintained during a transition of laboratory methods if the labs maintain a period of overlap of both methods and construct a model to relate the datasets.