Evidence of Omicron subvariant BA.2 likely detected in Saskatoon

A toxicology professor at the University of Saskatchewan believes he has found traces of the Omicron BA.2 subvariant, a potentially more-transmissible form of COVID-19, in samples taken in two cities in the province.

The Global Institute for Water Security regularly tests wastewater samples in Saskatoon, Prince Albert and North Battleford for evidence of COVID-19 in an attempt to determine whether case numbers are expected to rise or fall. The findings are then handed over to the provincial government and other researchers.

Researchers found three BA.2 mutations in samples of Saskatoon's wastewater taken on Jan. 2 and one BA.2 mutation on Jan. 9. Giesy said that means the BA.2 variant is likely in Saskatoon, but it may have only been in one person on those dates due to the low amount detected.

"We know they're specific for BA.2, but we don't have enough to have a consensus or to officially make the call," said Prof. John Giesy.

"It has been seen in other places in Canada, so it was only a matter of time until it arrived here."

There are a total of 26 mutations in the BA.2 subvariant. The team would have to find a minimum number of mutations in the wastewater in order to definitively say it had been spotted. 

Evidence of the BA.2 variant was also possibly detected in Prince Albert in early January, but has not been found in North Battleford so far.

Giesy said the Omicron variant quickly became the dominant strain of the virus. As a result, he said his lab is going to be on the lookout for the variant's progression.

"When Omicron came in, it went from nothing to 100 per cent in two weeks," he said.

"It took over very, very, very quickly."

Giesy said the BA.2 variant is approximately one-and-a-half times more transmissible than the BA.1 Omicron variant in the province right now.

In Ontario, the chair of the COVID-19 monitoring task force has predicted that BA.2 will cause a sixth wave of the virus in March.

"I don't know if I agree with that," said Giesy.

"I guess I would say I don't have an opinion right now. We don't have enough information to make that call."

Giesy said researchers are hard at work trying to understand the new subvariant. He said it's too early to tell if it has more severe effects than the original Omicron or will result in more hospitalizations.

He said his lab is not automated and it can take a while to do the gene sequencing. He then sends off the samples to the National Microbiology Laboratory in Winnipeg for confirmation, which can take several weeks.

While Canada is only seeing a slight uptick in BA.2 cases so far, other countries in Europe believe they have already started to see effects.

Denmark is reporting a new surge of BA.2 infections. In mid-January, the subvariant made up nearly half of all Omicron cases in the country, an increase of roughly 20 per cent since 2021.

Viral load up, but case numbers down

During the last wastewater study sent out by the University of Saskatchewan, Prince Albert, Saskatoon and North Battleford all saw increases in viral load from the last reporting period.

According to the Global Institute for Water Security, viral RNA load increased in Prince Albert's wastewater system by 358.4 per cent from the last time samples were taken.

Saskatoon saw an increase of 58.5 per cent and North Battleford saw an increase of 319.2 per cent in viral load.

The University of Saskatchewan samples were taken last week and predict the direction of cases seven to 10 days into the future.

Despite the spike in cases, Dr. Giesy believes that case numbers in all three cities will begin to decline by the middle of February.

"I was just looking at the numbers on the provincial dashboard and we're on track to have about 3,000 new cases this week, which is down a lot," he said in an interview.

"Our data peaked out about two weeks ago and has been trending downward ever since."

However, that prediction does not take the BA.2 variant into account and said cases may rise again as a result.

"My predictions have always been tempered by if nothing changes like government policies changing or new variants on the horizon we have been looking for."