SARS-CoV-2 viral titer measurements in Ontario, Canada wastewaters throughout the COVID-19 pandemic

Abstract

During the COVID-19 pandemic, the Province of Ontario, Canada, launched a wastewater surveillance program to monitor SARS-CoV-2, inspired by the early work and successful forecasts of COVID-19 waves in the city of Ottawa, Ontario. This manuscript presents a dataset from January 1, 2021, to March 31, 2023, with RT-qPCR results for SARS-CoV-2 genes and PMMoV from 107 sites across all 34 public health units in Ontario, covering 72% of the province's and 26.2% of Canada's population. Sampling occurred 2-7 times weekly, including geographical coordinates, serviced populations, physico-chemical water characteristics, and flowrates. In doing so, this manuscript ensures data availability and metadata preservation to support future research and epidemic preparedness through detailed analyses and modeling. The dataset has been crucial for public health in tracking disease locally, especially with the rise of the Omicron variant and the decline in clinical testing, highlighting wastewater-based surveillance's role in estimating disease incidence in Ontario.

Fig. 1

Geographical Overview of Sampling Locations in Ontario, Canada. This panel provides a broader geographical context, illustrating the location of Ontario within North America. (b) A comprehensive map of the province of Ontario, with its various public health units distinctly highlighted in various colors, demonstrating the diversity and range of health jurisdictions within the province. Northern Ontario is prominent in this panel, showcasing the public health units in this part of the province. Public health units of Northern Ontario: Thunder Bay District Health Unit, Sudbury and District Health Unit, North Bay Parry Sound District Health Unit, Northwestern Health Unit, Timiskaming Health Unit, Porcupine Health Unit, and Algoma Public Health Unity. (c) A detailed view of Eastern Ontario. Public health units of Eastern Ontario: Haliburton, Kawartha, Pine Ridge District Health Unit, Kingston, Frontenac and Lennox and Addington Health Unit, Peterborough Public Health Unit, Ottawa Public Health, Leeds, Grenville and Lanark District Health Unit, Renfrew County and District Health Unit, Hastings and Prince Edward Counties Health Unit. (d) A detailed view of Central Ontario and Western Ontario. Public health units of Central Ontario: York Region Public Health, Peel Public Health, Toronto Public Health, Halton Region Health Department, Simcoe Muskoka District Health Unit, and Durham Region Health Department l. Public health units of Western Ontario: Huron Perth Health Unit, Region of Waterloo Public Health, Southwestern Public Health Services, Lambton Public Health, Wellington-Dufferin-Guelph Health Unit, Brant County Health Unit, Middlesex-London Health Unit, Niagara Region Public Health Department, Chatham-Kent Health Unit, Windsor-Essex County Health Unit, Grey Bruce Health Unit, and Haldimand-Norfolk Health Unit.

Fig. 2

Longitudinal analysis of relative SARS-CoV-2 viral signal (expressed as the % of the max. viral signal) during individual VOC periods across major sampling sites in the Ontario wastewater surveillance initiative (WSI). The graph displays temporal trends in viral signal, expressed as a percentage of the maximum normalized viral signal measured throughout the studied periods (periods are delimited by variant of concern), at various key sampling sites. Color coordination is employed to highlight the magnitude of the PMMoV-normalized viral measurement (as a percentage) compared to the maximum magnitude of the PMMoV-normalized viral measurement during each of the periods, and to highlight peaks of viral signal, per variant of concern (VOC). It is important to note that while notable variations in the data may suggest fluctuations in virus prevalence, these should not be interpreted as direct correlations to distinct outbreaks or pandemic waves without further analysis. Particularly in later VOCs like BA.4/BA.5, and Omicron BQ/XBB-like, the patterns are complex with multiple high signal points. This visualization assists in understanding the spatial and temporal heterogeneity of SARS-CoV-2 prevalence in Ontario. Sites are ordered alphabetically, and site names are colored according to the laboratory which was conducting the testing. Gray sections with lines indicate data unavailability, and the data is resolution is weekly averages.