A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities
Shokoofeh Nourbakhsh,
Aamir Fazil,
Michael Li,
Chand S. Mangat,
Shelley W. Peterson,
Jade Daigle,
Stacie Langner,
Jayson Shurgold,
Patrick D’Aoust,
Robert Delatolla,
Elizabeth Mercier,
Xiaoli Pang,
Bonita E. Lee,
Rebecca Stuart,
Shinthuja Wijayasri,
David Champredon
Affiliations
Shokoofeh Nourbakhsh
Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
Aamir Fazil
Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
Michael Li
Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
Chand S. Mangat
One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
Shelley W. Peterson
One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
Jade Daigle
One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
Stacie Langner
One Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
Jayson Shurgold
Antimicrobial Resistance Division, Infectious Diseases Prevention and Control Branch, Public Health Agency of Canada, Ottawa, ON, Canada
Patrick D’Aoust
University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
Robert Delatolla
University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
Elizabeth Mercier
University of Ottawa, Department of Civil Engineering, Ottawa, ON, Canada
Xiaoli Pang
Public Health Laboratory, Alberta Precision Laboratory, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
Bonita E. Lee
Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
Rebecca Stuart
Toronto Public Health, Toronto, ON, Canada
Shinthuja Wijayasri
Toronto Public Health, Toronto, ON, Canada; Canadian Field Epidemiology Program, Emergency Management, Public Health Agency of Canada, Canada
David Champredon
Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada; Corresponding author.
The COVID-19 pandemic has stimulated wastewater-based surveillance, allowing public health to track the epidemic by monitoring the concentration of the genetic fingerprints of SARS-CoV-2 shed in wastewater by infected individuals. Wastewater-based surveillance for COVID-19 is still in its infancy. In particular, the quantitative link between clinical cases observed through traditional surveillance and the signals from viral concentrations in wastewater is still developing and hampers interpretation of the data and actionable public-health decisions. We present a modelling framework that includes both SARS-CoV-2 transmission at the population level and the fate of SARS-CoV-2 RNA particles in the sewage system after faecal shedding by infected persons in the population. Using our mechanistic representation of the combined clinical/wastewater system, we perform exploratory simulations to quantify the effect of surveillance effectiveness, public-health interventions and vaccination on the discordance between clinical and wastewater signals. We also apply our model to surveillance data from three Canadian cities to provide wastewater-informed estimates for the actual prevalence, the effective reproduction number and incidence forecasts. We find that wastewater-based surveillance, paired with this model, can complement clinical surveillance by supporting the estimation of key epidemiological metrics and hence better triangulate the state of an epidemic using this alternative data source.
