Advanced Analytical Platform for SARS-CoV-2 Wastewater Surveillance

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As of early May, 2022, the outbreak of COVID-19 had led to over 3.7 million positive cases and 39,200 deaths in Canada. Unfortunately, and especially with more contagious variants of concern (VOCs), performing current nasopharyngeal swabs testing at a population-wide level is impractical. Wastewater surveillance has been benchmarked as a cost-effective way to trace COVID-19 at the community level. Indeed, the UofT team, co-led by Dr. Hui Peng and Dr. Elizabeth Edwards, is currently monitoring SARS-CoV-2 trends in nine wastewater treatment plants that serve more than three million Ontario residents. However, the current wastewater SARS-CoV-2 surveillance approach is challenged by several limitations related to analytical methods and fundamental mechanisms. In the face of rising cases of the latest variant, Omicron, the need for more accurate surveillance is even more pressing. In the proposed project, the UofT team will develop an advanced analytical platform for SARS-CoV-2 wastewater surveillance by partnering with the Ministry of the Environment, Conservation and Parks (MECP), Toronto Public Health (TPH), Toronto Water and a commercial testing lab (SiREM). Three research objectives will be pursued in this project. First, a new sample enrichment method will be established by integrating three biorthogonal assays. The new sample enrichment method is expected to improve the sensitivity of the current SARS-CoV-2 wastewater surveillance by a factor of 10. We also aim to establish a novel LC-MS method for the rapid detection of new VOCs in wastewaters. This method may provide valuable advantages over qPCR and next-generation sequencing including short turnaround time, and high accuracy. Lastly, we will focus on elucidating the fundamental mechanism for the stability of SARS-CoV-2 viral RNA in wastewaters despite presence of RNases. Shotgun proteomics will be employed to identify which proteins complex with viral RNA in wastewaters. The analytical platform established through this proposed Alliance project is expected to advance SARS-CoV-2 wastewater surveillance, and will be adopted by MECP in a next phase of the Ontario wastewater surveillance initiative.