Researchers can now detect COVID variant in wastewater

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The wastewater test developed by CHEO Research Institute cell biologist Tyson Graber can be done more quickly and cheaply than the genetic sequencing currently being done in provincial labs to identify cases of B117 and other COVID variants of concern.

As soon as news got out, the phone calls and emails began. And then the poop arrived.

On Friday morning, the Ottawa lab that has come up with a test to detect the highly contagious COVID variant B117 in wastewater received a courier package — unsolicited — containing sewage samples. The package arrived just hours after the successful test for the B117 variant was mentioned on Twitter by some of Ottawa researchers involved. The samples came from a municipality desperate to find out whether the variant is present there.

“We need to send something to you now because we want to know,” said the note from the municipality, which suspects the variant is present in its community.

With that kind of anxiety growing across Canada about the more easily transmissible SARS-CoV-2 variants, two of which have been detected here, the test is a potential game-changer. And the excitement around it is palpable.

“I think it will save peoples’ lives,” said Patrick D’Aoust, the uOttawa engineering researcher and doctoral student who is part of the CHEO-uOttawa team working on wastewater surveillance. “It is kind of like a fire alarm. If we are able to get out warnings that this is creeping up before it is out of control, before it becomes the main viral strain, I think we are going to be able to save lives.”

The wastewater test developed by CHEO Research Institute cell biologist Tyson Graber can be done more quickly and cheaply than the genetic sequencing currently being done in provincial labs to identify cases of B117 and other COVID variants of concern.

“We can test a million people in Ottawa daily for the same cost as doing one test of (genetic) sequencing to detect if somebody has the variant right now,” said D’Aoust.

Unlike individual lab tests, wastewater testing samples for the virus in an entire population, even those with no symptoms, because virus is shed and can be detected in feces. Crucially, the results can offer public health officials a heads up about what is coming days before signs start to appear in lab tests. Wastewater testing could detect the presence of the B117 variant 48 hours or more ahead of current testing.

“The first priority is to be able to detect this earlier than we could normally with clinical testing,” said Graber, whose usual day job is genetically engineering viruses to kill cancer cells.

The research team received word that the test had worked late one Friday weekend about a week ago. The test, or assay, had successfully detected the B117 variant in a sewage sample from an Ontario community in which the variant is known to be present.

The confirmation launched frantic activity. Teams members have been working since then to test samples and share the information with others, so they can do their own testing. The researchers will publish a pre-print paper containing the information in the next few days.

“We want to disseminate the information so more people can apply it,” said Graber.

They have already tested wastewater in Ottawa and found no discernible levels of the variant. Three cases of B117 have been identified in travellers who have returned to Ottawa through clinical testing.

Graber and D’Aoust estimate that between 50 and 100 cases would have to be present in a city in order to get a detection through wastewater. Their findings suggest that, despite a small number of cases in Ottawa, the variant is not currently being spread through the community.

Wastewater in Ottawa will be tested several times a week for now, increasing to daily in coming weeks, they said. Ottawa is currently the only municipality in Canada that conducts and posts daily wastewater testing.

The lab is also doing regular testing for other communities in Ontario and working with researchers and labs across the country, some of which will begin testing for the variant in the coming days as well. Wastewater testing is also being done in some long-term care homes and other institutions.

The next step is to develop tests for other variants of concern — those originally detected in South Africa and Brazil.

Graber said he expects those tests to be developed in a matter of weeks. As with the B117 test, the challenge, he said, is to develop a test that picks out the specific genetic material that contains mutations associated with the variants.

This week, Public Health Ontario published a report on the prevalence of three COVID variants of concern — including B117 and those first detected in South Africa and Brazil. During one day of testing, Jan. 20, it identified more than 100 cases of the variants in positive samples. The majority were linked to a retirement home in Barrie where more than half of its residents have died from COVID-19.

Both Graber and D’Aoust have been pulled away from other research to help with the urgent work of testing and identifying COVID-19 in communities.

The work is significantly faster paced than traditional scientific research, out of necessity.

“We are trying to look through this fog and get the best answers we can as soon as possible. That is not the usual way science works,” noted Graber.

Both he and D’Aoust said the work is rewarding.

“The dream of every single scientist and researcher is you want to do something that is meaningful and you want to see results immediately,” said D’Aoust.

Graber added: “The immediacy factor is nice. Hopefully it is helping a little bit.”

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