New methods might be needed to catch COVID-19 virus variants in Manitoba

Manitoba might have to change the way it watches for concerning variants of the coronavirus that causes COVID-19, after a number of samples initially flagged as possible cases of a dangerous variant came back negative.

Current screening tools rely on genetic markers found in three known variants of concern. However, those markers are also found in other variants that are not considered a concern. 

Samples that are flagged in the initial screening process are then sent for full genomic sequencing, a labour-intensive process.

That's what happened earlier this month, when initial screening tests on samples from the Manitoba First Nations communities of Pauingassi and Pimicikamak detected a genetic mutation found in several known variants of the virus, including the more contagious B117 variant first detected in the U.K.

Those samples were sent for full genetic sequencing, and health officials determined they were another variant already found in Manitoba — one which has been deemed to have no clinical significance.

An easier way to detect the variant could be developing more specific primers — pieces of genetic material used to test for the virus — that won't confound the current testing method.

"I think it would be more feasible in terms of … labour and effort and money, to develop specific primers to cope with these mutations," said Carlos Farkas, a post-doctoral researcher at the University of Manitoba's Rady Faculty of Medicine who has studied variants and the challenges they pose to current tests.

Speaking at a news conference on Tuesday, Manitoba Chief Provincial Public Health Officer Dr. Brent Roussin said the tests need to be sensitive enough that they don't miss anything that could be a variant of concern.

"We want it very unlikely that we actually miss something we're looking for," he said.

Balancing sensitivity 

Designing a test to catch variants of concern is a matter of balancing sensitivity and specificity, Roussin said.

"We'll have to continue to work to ensure we have the right targets on our screening tests … to ensure that we're getting a bit more out of the screening tests," he said.

Manitoba laboratories have "plans to add additional markers that should be able to better distinguish variants of concern from local variants," a provincial spokesperson said. That's consistent with the Canadian COVID-19 Genomics Network's recommendations, according to the spokesperson.

As of Friday, when three new cases were announced, a total of four cases of the B117 variant had been identified in Manitoba. All four cases were travel-related, health officials have said.

Manitoba health officials aim to sequence around five per cent of the samples received, a number that is in line with other jurisdictions, according to a provincial government spokesperson.

In order to be confident they aren't missing variant cases in the community, the province needs to significantly increase the volume of samples it sends for genomic sequencing, said Nazeem Muhajarine, an epidemiology professor at the University of Saskatchewan.

"At some point, they need to get into more kind of random testing in order to really be sure about whether we are picking up the variants," he said.

Catching new variants

Viruses typically mutate as they spread, and most of those variations are inconsequential, virologists say.

But determining whether a new variant is one health officials should worry about is "not straightforward," said Farkas. 

One way is to study the way a virus behaves in a laboratory. Another is to observe how it is spreading in the community.

"If you live in a community where the community prevalence of COVID  is pretty high … that could also be another piece of information — a flag, if you will," Muhajarine said.

Pimicikamak, also known as Cross Lake First Nation, has struggled to contain a resurgence of the coronavirus in recent  weeks. In the span of two days, from Feb. 12 to 14, the number of active cases in the community nearly doubled from 42 to 82.

Dozens of recent cases have been linked to superspreader events in the community, including a birthday party, a wake and a funeral, band leadership said Friday. Overcrowded housing in the community is another cause, Chief David Monias told CBC News.

The B117 variant isn't the only one of concern Manitoba health officials are on the lookout for. The same genetic marker — known as N501Y — is also found in the two other major variants of concern, which were first detected in South Africa and Brazil.

Manitoba is waiting for a delivery of a new reagent, expected to arrive this week, that will enable screening for those variants as well, a provincial spokesperson said.