'All hands on deck': Montreal scientists step up in urgent COVID-19 variant hunt

Quebec hopes to curb spread of variants Those COVID-19 cases and hospitalizations are dropping, the province is looking to slow the spread of more contagious variants.

Montreal — Quebecers could perhaps be forgiven for being skeptical about new plans announced this week to drastically ramp up Quebec’s surveillance of COVID-19 variants.

That’s because of what had happened just a few days earlier. The province had said it found two cases of the highly contagious South African variant—or rather, it found them a month later, from an outbreak that occurred in Abitibi in early January.

If it takes five weeks to sequence the DNA of just two cases of the virus, what hope does Quebec have of sequencing every positive COVID-19 case in Montreal, about 3,000 per week right now, with a quick enough turnaround to make it count?

Lots of hope, it turns out. Quebec is unusually lucky in how much capacity it has to sequence DNA, with two well-equipped labs on top of the government lab, and all of them ready to help out.

“It’s all hands on deck,” said Ioannis Ragoussis, a professor and the head of genome sciences at the McGill Genome Centre.

McGill profs, students and other staff have been handling the majority of Quebec’s COVID-19 DNA sequencing, in fact—a workhorse in a system that divides tasks between the three labs and also asks hospitals around the province to pre-screen for variants.

DNA sequencing may be a delicate, complex process that most people only know through sci-fi movies, from Jurassic Park to Contagion. But it’s increasingly key to fighting the spread of COVID-19, if it can be done in big enough volumes.

It’s the only way to identify and ideally stop the spread of the three known variants—from the U.K., Brazil and South Africa—which are more contagious than the original COVID virus.

Montreal authorities announced this week that the city has 44 confirmed or suspected variant cases. On Thursday, Quebec Health Minister Christian Dubé said he wants to sequence the DNA of every positive case in Greater Montreal, though even he wasn’t sure it was possible.

“I was told that they could screen for the variants next week,” he said. “But at what level? I don't know—that’s what I don't know.”

A LUCKY PROVINCE

Nobody knows that yet, including those doing the sequencing—Ragoussis called the Montreal goal an “attempt”—but there’s still a lot of untapped capacity in Quebec.

The McGill lab is processing around 1,300 to 1,400 samples a week right now. That’s only about half of the total current weekly positive cases in Montreal, and the numbers are also meant to include sequencing of samples from around the province, not just the city.

But the Quebec public health institute, the INSPQ, also has its lab in Sainte-Anne-de-Bellevue, and a third one is being added to the mix in the coming days: Genome Quebec’s lab, based at the Ste-Justine hospital, which plans to be sequencing another 800 samples per week by April.

Three such labs is unusual. While the other major provinces might each have a lab or two, most smaller provinces don’t even have one.

The INSPQ government lab does some sequencing itself but also acts as the brain, crunching viral patterns across Quebec and telling the other labs which samples to retrieve and test, then analyzing the resulting DNA sequences. The other two labs do its bidding.

“We are putting all our capacity at the disposal of [the INSPQ] so we can sequence as many samples as possible, and develop new methods to do things faster and faster,” said Ragoussis.

“I spend a lot of time thinking [about] new technical development to do things faster and faster.”

The process starts in Chicoutimi, where every single positive COVID-19 test since the beginning of the pandemic remains stored in a biological bank run by Genome Quebec.

Once the requested samples arrive at the Montreal labs, specialized technicians prepare to feed them, in large batches, through a robotic machine.

The samples are divided up, then “we inactivate the virus, of course, because we don't want to spread the virus, even in the lab,” said Daniel Tessier, a vice president at Genome Quebec. The RNA must be extracted.

“The whole process takes about five or six days, then it's about one or two days of machine time, and then of course you have to do the analysis,” said Tessier.

DIVISION OF LABOUR, WITH RAPID-RESPONSE OPTION

While the three labs do what they’re asked by INSPQ as the pandemic evolves, they also seem set to handle slightly different tasks.

The INSPQ lab specializes in handling “difficult samples,” said Ragoussis. It includes “basically samples that have very low viral loads” and are therefore hard to analyze, but the government lab has a different method than most DNA-sequencing labs.

Genome Quebec, for its part, uses a standard system, but it will start small. It has committed to only 384 samples a week and a two-week turnaround for them, with plans to ramp up to 800 per week by April, then to 1,200, said Tessier.

“We’re starting to walk before we run,” he told CTV News.

Genome Quebec expects to be sent random samplings of positive COVID-19 tests, he said. Sequencing random samples is a form of surveillance: it can keep an eye on overall patterns.

"A portion of the samples are randomly selected from among all the samples positive for [COVID] in all regions of Quebec," the INSPQ confirmed in an email.

"Another part of the samples are selected in a targeted manner in order to maximize our chances of finding variants," the health institute said, including focusing on international travellers, existing outbreaks, post-vaccination COVID-19 infections, and people with "severe" illness.

The McGill lab, with its higher capacity, can do a bit of everything. But crucially, it rejigged its system this winter to create two streams: a regular-speed one and a fast one meant to sequence DNA in urgent, time-sensitive outbreaks.

“My lab is in a standby mode… we have a rapid-response unit,” said Ragoussis.

While results usually take a week or two, the fast stream is able to deliver sequencing "within a few days,” he said, which puts the McGill lab among the fastest in Canada.

Demand for the rapid-response sequencing has grown quickly in the past couple of weeks, he said, with several new and sensitive outbreaks, at schools or elsewhere.

The lab first designed its rapid-response stream for about 100 tests a week, but it’s done 300 just in the last week, he said.

WHY DID THE ABITIBI CASE TAKE SO LONG?

The news is less good for the remote areas of massive Quebec, which are likely to learn much more slowly than Montrealers if they have variants spreading, even without Montreal’s new sequencing campaign.

That’s because distance matters to processing speed. The multi-week delay before the South African variant was identified in Abitibi was likely due largely to the region’s remoteness.

Ragoussis confirmed that the Abitibi results only came back this week—there wasn’t a delay in when the province made it public—though he said he couldn’t say what the holdup was in that specific case.

Speaking generally, however, he said that “when things can get longer than expected is if there's a delay from collecting the samples… it could be shipping, it can be logistics of shipping, storing.”

As for ramping things up, it’s partly a question of labour, said Tessier. Many CEGEP-trained technicians have the basic skills necessary, though specializing, and the security skills to work with infectious viruses, does take extra training.

Ragoussian said that McGill’s staff have kept their academic work running, though at this point, it might be difficult to say which one is their side project—their own research, or sequencing Quebecers’ viruses.

We’re “working full-time now on this effort,” he said.