The laboratory in a downtown university building is under construction, its emergency wash station getting an upgrade, but the daily testing of incoming wastewater samples for COVID-19 goes on unabated.
Samples arrive in Nalgene-sized bottles from sites all over the city — large treatment plants and community and congregate sites, such as university residences, shelters and long-term care homes — and Nora Dannah has to walk down to shipping and receiving to collect them.
From there, a ritual-like process unfolds as she separates and spins, mixes samples with solutions and tells a robot to test (tracking the errors and redoing where necessary) before recording the specific details and the major trends of the pandemic.
“You have a protocol for everything here in the lab,” says Dannah, who completed a PhD in molecular genetics last year and now manages the day-to-day running of biology professor Kimberley Gilbride’s lab at X University (formerly Ryerson University, currently in the midst of a name change).
Gilbride teamed up with geography professor Claire Oswald to provide the university’s contribution to efforts to track the prevalence of COVID-19 in a particular community (or even a single large building) by testing its wastewater.
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That is, the teams are tasked with collecting human excrement at several different scales and to extract from it the ribonucleic acid (RNA) of the SARS-CoV-2 virus. From there, they can test it to see how much virus is present, whether it is one variant or another, and how these data points change over time.
Dannah, who has been working at the upstairs lab at Kerr Hall since September, says the work is easy but demands precision and consistency.
That means only she or one other senior staffer does the qPCR testing, which tells the story of how strong a viral signal is being sent through the sewers.
The team of a half dozen or so researchers and a couple of undergrads normally processes results on the same day it receives them. But it provides more by way of long-term trend than daily tally, ideally helping public health bodies and politicians better target vaccine drives or other policy measures to fight COVID-19’s spread.
(The City of Toronto publishes some of the data here.)
Even if “all of a sudden you are detecting COVID, it's good to run the sample or take the pellet and do RNA extraction (again) just to make sure they are real, solid results” that are confirmed the following week, Dannah said.
The process is done in triplicate and must also be replicable, which is why the samples are split into main and backup versions soon after arrival, later migrating to either a freezer, a deep freezer, or the centrifuge, where the pellets are made.
The pellet is poop (they test the samples for another common human fecal virus to make sure), but it’s also everything else that ends up down the drains of homes and businesses around town.
A primer solution is later introduced to the sample, which will cause a quantifiable reaction in the presence of the virus.
Public Health Ontario said in a report from April that wastewater surveillance had both pros and cons; it’s an independent signal from an entire population regardless of health status or ability to access individual testing, but it’s limited by a lack of standard testing measures and a reliance on collaboration between utilities, laboratories, and public health.
The data generated must also be interpreted within the context of both the sites and sources being sampled, the testing methods and laboratories performing the testing and the clinical epidemiology of the catchment area being sampled, it said.
Morgan Sharp / Local Journalism Initiative / Canada’s National Observer