New data shows Omicron was in Nova Scotia wastewater in November

A research team at Dalhousie University started detecting Omicron in Nova Scotia wastewater weeks before the COVID-19 variant was officially confirmed in the province.

"It was surprising to us to see a viral signal in early November. Only in retrospect were we able to see that it was a variant and not the original," said Prof. Graham Gagnon, director of the Dalhousie University Centre for Water Resource Studies.

The first Omicron case was reported in South Africa in late November. The first cases were confirmed in Nova Scotia on Dec. 13, linked to a COVID-19 outbreak at St. Francis Xavier University in Antigonish.

The virus survives longer in the gastrointestinal tract than in the respiratory tract, the university said last year, which means genetic material can be found in human wastewater even though COVID-19 is a respiratory illness.

The Dalhousie team has been testing wastewater for COVID-19 indicators since December 2020 at the Halifax region's four main wastewater treatment plants: Halifax, Dartmouth, Mill Cove and Eastern Passage, as well as the five student residences on the Dalhousie campus.

Gagnon was surprised to detect the virus last fall, because students who lived at the residences were required to be vaccinated and those who were being tested were getting negative results.

But he passed on the results to university officials, who used the information to warn students.

"For us it's been a successful project," said Gagnon. "It's a tool that can be used to help make decisions."

Similar testing is taking place in other parts of the country.

In Saskatchewan, the levels of the COVID-19 virus detected in the wastewater has increased by almost 88 per cent since Omicron was first identified in the province in December.

According to Gagnon, there has been a similar spike in Nova Scotia, but he did not want to be specific until the data has been double-checked.

"The concentrations were confusing to us initially because they are so high," said Gagnon. "It's unusual, so we want to do some quality assurance to be certain."

On Jan. 5, Nova Scotia Chief Medical Officer of Health Dr. Robert Strang said his team had had conversations with the Dalhousie researchers, but it turned out they had actually been "detecting the Alpha variant" and not Omicron.

"It's still a research tool that has yet to be validated in many ways," Strang said of wastewater COVID-19 testing.

Strang not aware of latest data

However, a provincial spokesperson clarified on Monday that Strang was not referring to the latest water samples. In an email, Kristen Lipscombe said Dalhousie University researchers identified two different wastewater samples as potentially containing the Omicron variant.

The first, taken in fall 2021, was confirmed to contain the Alpha variant and not Omicron. The second sample was taken in early December and sent to the province's public health team on Jan. 4. 

Lipscombe said Strang had not received information about the second sample at the time of his comments, so he was referring only to the first sample.

"Results from the second sample are suggestive, but not conclusive, that Omicron is present in wastewater, but this isn't surprising given current community spread of this variant," Lipscombe said.

Research Nova Scotia has provided funding for the wastewater testing project. The work wraps up in March.