A new testing process in Ottawa has detected the COVID-19 B.1.1.7 UK variant in Barrie’s wastewater and ongoing screening could find early indications of any increases in infections.
Regular testing in the weeks and months ahead by two different laboratories will provide something of a barometer to show whether the incidence of COVID-19 as well as the variant is becoming more — or less — of a concern.
Last week, the City of Barrie joined the provincewide Wastewater Surveillance Initiative for COVID monitoring in municipal wastewater, which analyzes samples from the municipality’s wastewater treatment facility.
Orillia, Collingwood and Midland are also sending untreated wastewater samples to the Ontario Tech University laboratory in Durham Region, which determines the amount of COVID present in the wastewater before it’s treated.
A second, new laboratory test at the University of Ottawa developed with the Children's Hospital of Eastern Ontario (CHEO) allows for quick detection of the UK variant, which is now being applied to samples collected in Barrie.
The UK variant, which is behind the deadly outbreak at the Roberta Place long-term care home in Barrie, is reported to be more easily transmissible.
The long-term care home in the city's south end has been in outbreak since Jan. 8 when it was declared by the Simcoe Muskoka District Health Unit. Since early January, 69 residents and one essential caregiver linked to the home have died after contracting the virus.
According to a health unit update on Wednesday, overall in the region there are 133 cases that have tested positive for the UK variant, which is unchanged from yesterday's report, and an additional 86 cases have screened positive and are awaiting confirmatory testing, which is up from 64 on Tuesday.
Examining sewage for clues
Measuring raw sewage for levels of the SARS-CoV-2 RNA genetic material allows detection of the presence of the virus in the entire population before it would otherwise become apparent.
The screening shows what’s happening in the community when the virus is shed through feces and travels into the municipality’s sewage system to be treated.
“What’s great about it is it captures asymptomatic people and people who aren’t getting tested,” said aquatic ecologist/microbiologist Andrea Kirkwood of Ontario Tech University, where testing of samples from the four Simcoe County municipalities, as well as eight other sites, is being conducted.
“We usually pick up the signal before the hospitals see the cases start to increase," she added.
Three samples per week from the wastewater treatment plants are currently being analyzed to detect the presence of COVID-19 in the community using a sensitive technique called polymerase chain reaction (PCR).
By monitoring the results of the samples over time, Kirkwood expects to report early indications of any trends in a couple of weeks.
The data is being shared with the Simcoe Muskoka District Health Unit and a dashboard is currently in development.
The testing will also show the presence of variants in the wastewater, but no specific primers are being used at that lab at the moment to show anything more specific.
Samples from Barrie’s wastewater treatment facility are also being sent directly to the University of Ottawa, which zeroes in on the UK variant.
Those who developed the process at the Ottawa lab started using their new method on samples from Ottawa. When that failed to provide any noticeable indication of the UK variant there they approached officials in Barrie.
“We happened to develop this assay (analysis) and when the news broke about the situation in Barrie, that’s when we said maybe we should try to apply this there and see if we could actually validate that it works and then maybe apply it to areas to help out and make a difference,” University of Ottawa professor Robert Delatolla said from the Ottawa lab.
In addition to collecting samples from the general wastewater, city officials also sent a sample collected from the sewage system near the Roberta Place long-term care home on Essa Road.
Acting on the results
For Simcoe-Muskoka medical officer of health Dr. Charles Gardner, the new partnership with the City of Barrie, the University of Ottawa and CHEO is another tool, a sort of early warning system for any surge in cases.
Through the ongoing — and what he hopes is frequent — testing, they expect to see the amount of activity of the virus and its variant here, whether it’s circulating freely in the community and whether they have control of the situation.
“I would like that to be done in some of our other communities as well,” Gardner said.
The experience for Ottawa Public Health, he said, is testing of wastewater often shows indication of any concerns in the community early on.
Gardner described it as a surveillance tool which helps answer the question: What’s happening with the UK variant?
Testing people provides a limited ability to glean answers and show spread of COVID-19 and any variant. But this approach shows the broader implication, earlier on.
“We’d have a higher degree in what we know if we also had the results of wastewater testing,” he said.
UK variant testing
It’s a quick process, returning results for the variant within a day, says Delatolla, pointing out genetic sequencing conducted in provincial labs to detect specific variants usually takes three days to return results.
“Once you’re able to give your results quickly to public health, all of a sudden it’s potentially actionable. People can now use it and see it in the right period of time” to make decisions, the professor said.
The Ottawa lab — which is a collaboration between the University of Ottawa and the CHEO Research Institute — has been screening wastewater for COVID-19 since April. But then cell biologist Tyson Graber, who is a member of that team, was able to develop a way to specifically look for the B.1.1.7 or UK variant.
Through frequent sampling, researchers are able to see the signal for both COVID-19 and the variant go up or down.
“Sometimes that signal in the wastewater can even lead what you see clinically. There’s asymptomatic people who fecally shed, there’s all sorts of people who don’t get tested, there’s pre-symptomatic people who fecally shed in the capture basin of where the sewers are in the area,” he said. “And that’s what we’re doing with Barrie’s wastewater.”
The Barrie samples are 24-hour composites, which is a mixture of wastewater collected at various times of the day, providing an overall indication of the day’s events.
Three different samples have been tested — which is also done through the PCR method — and more are expected, but the scientists say that’s not enough to provide even an early indication of what’s happening with that variant in the community.
Delatolla did have the National Microbiology Laboratory sequence the Barrie samples, which confirmed their findings.
Meanwhile, the method is being shared and there are collaborations with universities across the country with the expectation that more communities will have similar testing conducted.
The work at the Ottawa lab is funded through the Ontario Ministry of the Environment, Conservation and Parks’ Wastewater Surveillance Initiative and is expected to expand to develop wastewater testing methods for other variants.
“Hopefully you’re going to see tools like this, from wastewater, come into play and help us as a province,” said Delatolla. “We’re already working on the next variant.”
Looking at what the human body discards into the wastewater system provides a variety of bio indicators, Kirkwood points out.
In the past, examination of wastewater has detected indications of diabetes as well as opioids and other drugs and overall public health. But the current process allows for more immediate action.
“This has kind of opened up a whole new way to monitor public health,” she said. “From a research perspective it is very interesting to us if there are other indicators that correlate with SARS-CoV-2 that maybe hasn’t been picked up.”
There is hope that the new programs will continue in the long after the crisis passes so that officials can be alerted of any indication of any reemergence of detectable cases.