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Ontario SARS-CoV-2 Variants of Concern Surveillance in Wastewater Pilot Program

COVID-19 Regional Genomics Initiative
Genome Centre(s):
Ontario Genomics
Project Leader(s):
Lawrence Goodridge (University of Guelph), Robert Delatolla (University of Ottawa)
Fiscal Year Project Launched: 
Project Description: 

In Ontario, variants of concern (VOCs) now account for 67% of all Ontario SARS-CoV-2 infections. SARS-CoV-2 variants of concern (VOCs) are quickly out-competing endemic, ancestral variants in a number of regions around the world due to significantly increased transmissibility (Coutinho et al. 2021). Escape from natural immunity (e.g., those previously infected with an earlier variant becoming reinfected with a VOC) as well as vaccine-induced immunity is a growing concern. In Ontario, VOCs are associated with a 63% increased risk of hospitalization, a 103% increased risk of intensive care unit (ICU) admission and a 56% increased risk of death due to COVID-19 (Ontario Science Advisory Table 2021). Current approaches to identify VOCs are based on quantitative real time polymerase chain reaction (qRT-PCR) analysis and genome sequencing of clinical samples. The attack rate of VOCs is so high that the slow speed and biases associated with traditional clinical testing precludes an accurate and timely reporting of VOC incidence to PHUs. Additional population-level metrics, independent from clinical data are needed to provide PHUs with actionable information. Wastewater-based detection of VOCs using qRT-PCR and sequencing methods is an untapped information source that can fill this need. In addition, the identification of VOCs in wastewater will provide information regarding the presence of VOCs in communities, since wastewater samples include fecal waste from many people, and multiple variants are likely to be found in each wastewater sample.

A focused Ontario VOC Surveillance in Wastewater pilot program will provide valuable data for early detection, trend tracking, and community risk assessment. The objective of this proposal is to mobilize a core group of researchers to develop and apply an Ontario-wide SARS-CoV-2 VOC wastewater surveillance program, that consists of qRT-PCR analysis of wastewater for VOCs followed by genome sequencing of qRT-PCR positive samples, for in-depth tracking of known and emerging VOCs. The pilot program will mobilize existing teams with expertise in the province for the application of the qRT-PCR assays to perform surveillance of SARS-CoV-2 VOCs across the province. Samples will be analyzed by qRT-PCR in all provincial regions bi-weekly, and samples from each region will also be analyzed for VOCs by sequencing. If the sequencing data demonstrates a new VOC for which a qRT-PCR assay does not exist, then a new assay will be rapidly designed for roll out to the team members conducting qRT-PCR surveillance. Wastewater VOC surveillance is a complementary approach to clinical surveillance with current critical partnerships with municipal, provincial and federal public health being leveraged to ensure the timely dissemination of SARS-CoV-2 VOC data from wastewater. This information will be used to help guide decision-making for communities in Ontario, improving the public health response to the COVID-19 pandemic.