On November 24, 2021 (epiweek 47), the Ontario wastewater surveillance initiative (WSI), a province-wide COVID-19 surveillance program, sprang into action. One day prior, reports of a high incidence SARS-CoV-2 variant in South Africa with Pango designation B.1.1.5291 led the WHO to swiftly assign it as VOC Omicron on November 262. Thanks to capacity and expertise built during the COVID-19 pandemic, WSI and Public Health Agency of Canada (PHAC) researchers quickly implemented metagenomic sequencing3 and allele-specific qRT-PCR to detect and quantify Omicron-specific viral fragments in wastewaters representing the major population areas of Ontario (Figure 1).
Measurement of Omicron incidence via wastewater
The first cases of Omicron in North America were identified in Ottawa, Ontario on November 28, 20214 through Public Health Ontario’s clinical genomic surveillance program which was prioritizing sequencing of test-positive travellers. On December 8 (epiweek 49), WSI reported its wastewater-based findings to Ontario’s Office of the Chief Medical Officer of Health as follows: WSI and PHAC researchers found no conclusive evidence of omicron signature alleles at any of the Ontario sentinel sites reporting prior to or during epiweek 47. In epiweek 48, the City of Kingston (East Health Region) experienced an Omicron outbreak first confirmed and monitored by clinical surveillance coincident with increasing SARS-CoV-2 signal in wastewater.
Low frequency sequencing of wastewater samples during this dynamic period was supplemented with rapid implementation of bespoke qRT-PCR assays (targeting N:P13L, N:R203K, N:G204R) in epiweek 49 at laboratories servicing municipalities in East and Central West Health Regions. The strategy of deploying qRT-PCR, prior to or together with sequencing, provided real-time estimation and reporting (within 24 h of sampling) of increasing Omicron allele frequencies in epiweeks 48 and 49. The WSI implemented a similar plan of action during the Alpha and Delta waves5. Further, decreasing Delta allele frequency was observed and tracked at this time through metagenomic sequencing and a bespoke qRT-PCR assay targeting the N:D63G diagnostic mutation (Figure 1).
Concurrent with VOC frequency estimation, WSI laboratories continued to report near real-time (frequencies ranging from daily to weekly) measurement of variant-agnostic SARS-CoV-2 signal across sampled sites (Figure 1, right panel; using CDC N1 and N2 or E qRT-PCR assays). Thus, within 2 weeks of learning Omicron’s existence, the WSI confirmed: 1) Omicron was not prevalent across Ontario prior to epiweek 49, and 2) SARS-CoV-2 viral load was low and stable across the province. These findings, obtained independently from clinical surveillance, provided timely situational awareness to municipal, regional, and provincial authorities; pointing to a low and stable COVID-19 community health state in Ontario prior to broad Omicron attack.
Correlation of clinical and wastewater COVID-19 indicators
Preliminary comparison of province-wide clinical SGTF frequency estimates retrospectively analyzed December 28, 2021, and wastewater-based Omicron frequency estimates retrospectively analyzed at the time of submission, revealed that these independent measures correlated well with each other across time. A province-wide analysis of both clinical and wastewater-based surveillance showed that Omicron had supplanted Delta in much of the populous Southern portion of the province by epiweek 51, only 2 weeks following its first detection in travellers through clinical genomic surveillance.
Inferring falling inflection point and forecasting peak hospitalizations
Due to the high incidence of Omicron in Ontario entering epiweek 51, universal clinical testing capacity was quickly saturated and case tracing overwhelmed. Restricted testing to high-risk individuals and those working in high-risk settings beginning December 31, resulted in underestimated cases and the inability to accurately identify a falling point of inflection along the epidemiological curve6. Province-wide estimation of SARS-CoV-2 RNA levels in wastewater (a population-weighted, aggregated dataset representing samples analyzed at 101 wastewater treatment plants, pumping stations and sewer shed access points within the WSI network) reported around January 12, 2022, indicated that the peak of the Omicron wave had been reached (Figure 1, right panel). Population-weighted aggregated signal is biased towards dense urban centres such as Toronto. Because population density across the province can vary by one order of magnitude, this can mask antipodal trends observed in less populated regions. Decision makers are therefore cautioned that both state- and city/region-level data should be evaluated in any decision-making framework that relies on wastewater-based surveillance.
Provincial and regional breakdowns of wastewater-based SARS-CoV-2 signal trends, along with clinical measures, are updated weekly and available at https://covid19-sciencetable.ca/ontario-dashboard/#wastewatersignal . Approximately 2 weeks following the observed decrease in wastewater signal, the number of hospitalized patients testing positive for COVID-19 appeared to have reached a peak and was beginning to decline. The number of hospitalized patients with COVID-19 in Ontario has since continued to decline, mirroring the SARS-CoV-2 wastewater signals that were observed several days prior.