Omicron surveillance key as Alberta tries to control new, worrying variant

As Alberta's omicron case count ticks up, scientists at the provincial lab are working to identify cases and preparing for the possibility the new variant could take hold in the province.

As of Monday afternoon, Alberta Health had reported a total of 11 cases of omicron, 10 of which were identified in returning travellers and one in a household contact of a traveller.

According to Alberta Health, all of the people who have tested positive have mild symptoms and are recovering at home.

The province had reported a total of 12 cases earlier in the day but revised the tally after receiving word one of the positive cases is not an Alberta resident.

The discovery of these cases has taken no one at the provincial lab by surprise.

"We were fully expecting it. We were ready for that," said Dr. Graham Tipples, medical-scientific director of the Alberta Precision Laboratories public health lab.

"We know when we hear about things internationally that we immediately start planning and figuring out how we would deal with it if arrived in Alberta, and sure enough, it came pretty quickly."

One critical step involved resuming screening all positive COVID-19 cases for key variants of concern on Nov. 24 as concerns about omicron emerged.

The lab stopped doing that on Sept. 10 as case counts soared during Alberta's fourth wave, and focused on targeted screening of groups including travellers and hospitalized patients, instead.

With no quick screening test for the omicron variant, all cases that come back negative for delta during that initial screening test are now sent on for more complicated genome sequencing to look for omicron.

All non-delta cases go through full genome sequencing, a painstaking and data-heavy process which can take two weeks, and the lab has the capacity to conduct this full sequencing on 800 to 1,000 cases a week.

But in order to speed up the confirmation process, the provincial lab is also doing rapid sequencing of all non-delta cases — which takes, on average, four to five days.

This process involves sequencing just the spike gene (S gene), which is the key area of concern in the omicron variant because it is characterized by more than 30 different mutations.

"Our research team in Calgary, as soon as we've got, 'hey, this could be an omicron from our screening assay,' they immediately jump on that and they sequence the S gene," said Tipples.

Alberta's first omicron case, he said, took about 24 hours to confirm through rapid sequencing.

"You can do that for a case here, a case there, a case there — which you have when something is emerging. Having that degree of effort on a single sample, and that timeliness for essentially stat testing, is absolutely impossible if you're looking to do it for all," said Tipples.

Planning for quicker test

The microbiologists, scientists and lab technologists at the provincial health lab have been down this road before with other variants, and are currently preparing for the possibility omicron could gain a foothold in Alberta.

They're pouring over data from other countries with more cases of omicron so they can develop a quicker screening test if needed.

"We're certainly looking into potentially designing a faster screening test for it that would compliment the whole genome screening that we're currently doing, and provide the opportunity for more rapid detection," said. Dr. Nathan Zelyas, a medical microbiologist with the public health lab.

"But we really do need to go back and look and see that overall genomic data that's coming out from the areas that are reporting it — what they're coming out with … it's still very much a work in progress."

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The lab has ordered the supplies it will need for a faster screening test, in case it is deemed necessary.

"If we truly needed an omicron specific screen, we're doing the work now to be able to set up to do that. It remains to be seen whether we do need an omicron specific screen. I think time will tell on that," said Tipples.

According to Tipples, a faster screening test for omicron might be needed if the new variant takes hold and the genome sequencing system can't keep up with demand.

"Certainly, if it started to establish in the province and you're really trying to keep a close eye on how much spread there is in the community, then that would make sense for a period of time," he said.

With so many questions surrounding the omicron variant, Dr. Dan Gregson, an infectious disease specialist and associate professor in the Cumming School of Medicine at the University of Calgary, said surveillance will play a key role early on.

"Right now it's important so we know how much is coming into the community, whether we're having community transmission," he said.

Part of the problem currently is that it is unclear how effective vaccines are against omicron. It's also unknown which monoclonal antibody therapies — treatments designed to boost the body's immune response — will work against it.

According to Gregson, some therapies have proven effective against only particular variants.

"Knowing which variant you have has an effect in terms of which monoclonals you use … it becomes important to know which variant one has, in terms of therapy. That's important when you start dealing with sick patients," he said.

"When you're dealing [with omicron] in the community, really it's a question of, are you isolating people and quarantining people differently with one variant versus another."