The scene inside Ontario’s overwhelmed labs
Not enough trained staff, testing supplies and even space resulted in a massive COVID-19 testing backlog
Over the summer, as the rest of the country opened up and slowed down, and the spectre of COVID-19 began to fade, life inside Ontario’s large medical laboratories continued to accelerate on a kind of perpetual motion pace, building speed and building size without ever slowing down, no matter what came in, who showed up or whether anyone could find any room for the new machines.
In Mount Sinai Hospital, in Toronto, Dr. Tony Mazzulli, the hospital lab’s microbiologist in chief, was busy hiring techs, finding supplies and keeping one wary eye on the fall. Mazzulli, like other lab leaders, public health experts and infectious disease specialists, knew that when the weather changed, a spike in COVID cases would follow. He spent the summer working with colleagues in his own lab and across the system to process the samples coming in every day while continuing to expand an ad hoc lab network that had already mushroomed in capacity multiple times since March.
“The labs really didn’t get a break through the summer at all,” said Dr. Kevin Katz, the medical director of Toronto’s Shared Hospital Lab, one of the largest in the province. “The volumes just kept going up, up, up. On the hospital side and across the whole system, everybody was able to take a little breath. The labs just kept grinding and implementing and growing.”
The Sinai lab alone overtook a classroom, added machines and technologists and expanded into a 24- houra- day, seven- day- a- week operation. It grew from a COVID rounding error in March, capable of processing 600-700 molecular PCR tests in a day, to a pillar of Ontario’s COVID testing system. By late spring, the lab’s technologists were analyzing 3,000 to 4,000 tests every day, Mazzulli said. They already had the space, staff and equipment to handle as many as 10,000 samples daily at that point and plans were in place to bring that number up to 17,500 by mid- October.
For a time, the lab seemed on track to meet that target. Then it “sort of derailed for a number of reasons,” Mazzulli said.
The second wave of COVID-19 overwhelmed multiple parts of Ontario’s pandemic response system. When schools reopened in the fall, testing centres across the province were crushed by the surge in demand. The province scrambled to make more swabs and pop- up centres available. But that effort didn’t make the bottleneck disappear. Instead, it just moved it further down the line.
By late September, the network of public health, hospital and private labs that process COVID tests in Ontario was dealing with tens of thousands more samples every day than it could push through in any 24-hour-period.
A pop-up testing centre at the Islamic Institute of Toronto in Scarborough, Ont., on May 29.
THE CANADIAN PRES/ Nathan Denette
WE GOT APPROVAL TO GO AHEAD AND PURCHASE THE EQUIPMENT, BUT THEY DIDN’T GET APPROVAL TO MAKE THE RENOVATIONS TO THE LAB. AND SO UNTIL THAT CAME IN (IN SEPTEMBER) OUR HANDS WERE A BIT TIED. — DR. TONY MAZZULLI
The result was an ever- growing backlog of unprocessed tests that peaked at more than 90,000 in early October.
The Ontario lab system has been a mostly invisible player during the pandemic. But if there’s one thing the fall surge made clear, it’s that nothing else in the system, not testing, not tracing, not suppression of the virus itself, can work if the labs fall behind. The autumn backlog then stands as both a critical failure and a crucial opportunity to learn. The virus isn’t going away soon. More waves will come. So what went wrong, and why?
To better understand those questions, the National Post spoke to the heads of some of Ontario’s most important labs in the public health, hospital and private systems, as well as veterans of Ontario Public Health and leading outside experts. Together they paint a picture of a system doing often extraordinary things despite immense barriers and sometimes iffy provincial leadership.
Through the spring and summer at Sinai, they couldn’t find enough trained staff; Ontario has long had a chronic shortage of licensed laboratory technologists. Testing supplies, too, were an endless issue, and not just for Sinai. “We have grappled with every single piece that we use for the testing process,” said Dr. Larissa Matukas, the head of microbiology at Toronto’s St. Michael’s Hospital. “Just when you think you have reagents, they disappear. Just when you think you have the plastic wear, it’s gone.”
For Sinai, one of the biggest issues was literally just space. The lab wasn’t physically big enough for the job it needed to do. So months before the fall rush, Sinai, along with other big labs, asked the Ontario government for the money it needed to expand. And for months, according to Mazzulli, the province sat on that request. “We got approval to go ahead and purchase the equipment, but they didn’t get approval to make the renovations to the lab,” Mazzulli said. “And so until that came in ( in September) our hands were a bit tied.”
When the fall COVID rush did arrive, on schedule and as predicted, Sinai had the staff and the equipment ready, but they didn’t have the room. “We do have four analyzers sitting in storage, which we can’t bring in physically to the lab until the renovations are done,” Mazzulli said in early October.
Sinai wasn’t the only lab in that position. Hospital and public health labs submitted a budget proposal outlining the anticipated surge and the money needed to deal with it sometime in either late spring or early summer, said one source with deep knowledge of the system. But it wasn’t approved until after the second wave hit in the autumn. “Heels were dragged,” the source said. “And that’s awful. Because it’s not a light switch. You don’t just say, ‘ Great, I’ve got the money. I can increase the diagnostic testing capacity.’ It doesn’t work like that. It takes about two to three months.”
The province has since taken steps to cut the number of tests coming in, but the backlog, while it lasted, took a brutal toll on Ontario’s COVID fight. “As recently as two weeks ago, we were getting less than 20 per cent of positive cases reported to us within 24 hours from the labs, and less than 50 per cent of cases reported to us within two days,” said City Councillor Joe Cressy, who chairs the Toronto Board of Health.
At that speed of return, the testing system was all but cosmetic. It was like giving a virus that doesn’t need any kind of edge a 50- metre head start in a 100- metre dash. “To put it simply, the combination of insufficient testing, coupled with delays in lab reporting, significantly constrained our ability to do contact tracing and our collective ability to prevent a significant second wave,” Cressy said.
“I actually think that we’ve done this in lightning speed. This is unprecedented,” said Matukas at St. Michaels. “It is unprecedented for us to expand lab capacity at the pace that we have over the past seven months. I know we’ve been using that word a lot during this pandemic, unprecedented ... But I have never participated in anything that moved so fast, so quickly and still maintained the level of quality and robustness it would have if we had done this more slowly and meticulously.”
Like many aspects of Ontario’s COVID response, those efforts have been hampered by both chronic issues — some of which go back decades — and a provincial leadership that critics say has moved too slowly, too often during the pandemic.
Those critics argue the province should have seen the fall surge coming and acted sooner to both cut demand for testing and prepare labs for the surge. “It’s a simple volume versus capacity issue,” said Dr. Dominic Mertz the medical director of infection control at Mcmaster University in Hamilton. “We knew that with respiratory virus season starting, we would have many more people symptomatic, regardless of what COVID is doing. So we anticipated that. But the ramp up of testing capacity hasn’t happened. The focus was, I would say, on other things over the summer.”
The province’s monthslong delay in approving new infrastructure funding was part of that failure, lab leaders agree. But it wasn’t everything. “Certainly money is one of those factors that if we had it sooner and earlier it would have helped us to maybe secure more stuff, more real estate, those renovations, and certainly get to where we need to get to,” said Matukas. “But then we still have all the other things like, where are the human resources? Where are the supplies and reagents? And what are we doing to really manage the demand?”
The simplest thing the province could have done, critics argue, wouldn’t have cost any money. In fact, it would have saved cash. The province waited until after the testing system was overrun this fall to walk back the message that anyone who wanted a test could get a test. That was a crucial error, many experts believe. “There’s really only two categories of people who need testing. And those are individuals who are symptomatic and individuals who have been in contact with somebody who is known to have COVID,” said Matukas.
All those unneeded tests made the fall surge worse. But even without them, the labs would almost certainly have been overrun at some point. Matukas said the best estimates for how many people are walking around with COVID- like symptoms during cold and flu season in Ontario are somewhere between 50,000 and 100,000. The province has never been able to sustain daily testing even at the bottom end of that range.
Why not? Supplies are a big part of it. Molecular PCR tests are incredibly resource intensive. And almost everyone on earth right now is competing for those same resources. “It’s basically amplified from what it was in March,” said Dr. Vanessa Allen, Public Health Ontario’s chief of medical microbiology and laboratory sciences.
One problem that has cropped up repeatedly since March is that some of the best, most efficient instruments for processing COVID samples operate on proprietary systems. The Public Health Labs, for example, use several machines manufactured by Roche, the Swiss health- care giant. A single, high- throughput Roche instrument can handle up to 3,300 tests in 24 hours. But the catch is they only work with Roche supplies.
This isn’t just a Roche issue, either. All the proprietary instruments from the major manufacturers work that way. And all of them, at some point during the pandemic, have had supply chain issues. “All of the supplies: pipette tips, plates, reagents, tubes, just everything ... is under pressure.” Katz said. “If you run short of one piece of that whole process, the whole line comes to a halt.”
If you run short of one piece ... the whole line comes to a halt.
OUR BROAD APPROACH TO TESTING HELPED US DETERMINE IF AND WHERE COVID-19 WAS SPREADING. WHAT WE FOUND WAS THAT IT WASN’T WIDELY CIRCULATING IN ANY COMMUNITY . THIS WAS AN IMPORTANT DECISION TO TARGET OUR RESOURCES . — DAVID JENSEN
To reduce that friction, the Public Health Labs, under Allen, have been buying exclusively non- proprietary instruments since February. That allows them to mix and match supplies for different parts of the operation from different suppliers, some of them domestic. But the so- called open systems just aren’t as powerful as the best proprietary machines. A single, open- system instrument, fully stocked and staffed, can only process 1,854 samples in a day, just over half what the Roche machines can do. “When we do have reagents ( the Roche machines) are phenomenal workhorses,” Allen said. “So we’re not ready to abandon them entirely.”
Staffing, too, has been a constant problem. A molecular PCR test is not a simple procedure. It’s not like a pharmacy- bought pregnancy test. It takes real expertise to both conduct and interpret.
Most of that work has to be done by licensed laboratory technologists. But since at least the 1990s, Ontario has had a severe shortage of those kinds of techs. The issue, according to Michelle Hoad, the chief executive of the Medical Laboratory Professionals Association of Ontario, goes back to a decision made in the 1990s to close seven of the province’s 12 programs for training technologists. At the time, she said, there was a view that as lab processes got more automated, fewer humans would be needed to work in each lab. But it hasn’t worked out that way.
Garth Riley, who retired as the director of Ontario’s Public Health Labs in 2015, said that issue was known and talked about at the highest levels of the organization for most of his tenure there. “And it still hasn’t been addressed properly in my opinion,” he said. There have been more recent warnings, too. For the last 18 months, Hoad and her colleagues have been meeting with the government, trying to get them to do something about it. “I don’t think it was taken as seriously as it should have been,” she said. “And then COVID hit.”
There is only so much the labs can do about the shortage now. To help with the load, some retired technologists have come back to the job. Labs have also shifted some tasks to less specialized assistants. The technologists that are available, meanwhile, have been working incredible hours. “They are the unsung heroes of the pandemic,” Katz said.
But staffing is just one of several chronic problems that have long dogged Ontario’s public health lab system. Those issues have almost certainly hurt its ability to the respond to the pandemic, Riley believes.
After SARS, the public labs were incorporated into the new, arm’s length Ontario Agency for Health Protection and Promotion, the precursor to today’s Public Health Ontario. The labs at that time, “were kind of an unwanted child,” Riley said. For a time they flourished in their new, quasi- independent home. But within a few years, the government began to claw them back in. Eventually, Riley said, “you couldn’t spend a penny without getting the approval from the ministry of health. And as a lab, working with the ministry of health was always challenging because these people did not understand laboratories.”
Money was another constant issue. “The public health labs were always underfunded. And the budget was capped for several years,” said Dr. Natasha Crowcroft, who was Public Health Ontario’s chief science officer until late last year. That left the network already overstretched and underfunded when the pandemic hit.
Crowcroft, who now works for the World Health Organization in Geneva, blames successive governments for that problem. But she thinks Ontario’s public health leadership bears some responsibility too. “The strategy of the organization when it ran into financial problems was to try and keep quiet about them so they didn’t get into trouble with the government,” she said. “And I think that strategy ... is what meant that they were not in a good position when this hit. When other organizations were pushing back against cuts, Public Health Ontario wasn’t. So I think there has been a failure of leadership.”
Those budget constraints have had a real impact. Almost two decades after SARS, to cite one example, Ontario came into the COVID- 19 pandemic still without any kind of unified, digital system for the different labs to communicate with each other. As a result, the public health, hospital and private health labs are still manually filling out and filing tens of thousands of paper requisitions every day.
It would be hard to exaggerate how big a data problem this has created. “Colleagues of mine at another lab said that for every lab technologist (working) they have 2.4 people doing data entry,” Allen said. At Mount Sinai, the lab took over an entire, 1,000 square- foot classroom just to house 20 new data staff.
That this issue is still lingering, even now, doesn’t surprise Riley. “The public has a short memory. The government has even a shorter memory,” he said. “So that’s sort of how we got to where we are.”
Even given all those problems, many observers believe that what Ontario’s laboratories have accomplished over the past seven months is nothing short of remarkable. They’ve built, effectively from scratch, a coordinated network of labs from different organizations and different cultures that is now performing tests at a speed and on a scale never before seen in this province.
The massive backlog that happened in the fall was the result of long- term problems that were exacerbated by short- term issues, some of them preventable, some not. “I think what happened there was that there was a mismatch between just the pure capacity on the instruments and the labs and the number of tests that were being collected and coming in,” said Katz.
The Ford government could have done more to prevent that from happening, It could have spent more money, sooner, to bring more lab capacity online. But that doesn’t take away from the things those working in the system have managed to do. “We have really moved a lot of mountains together,” Allen said. “But there’s still a long way to go and I’m not downgrading that.”
The National Post sent a list of detailed questions to Ontario Health, Public Health Ontario, and Health Minister Christine Elliott’s office about this story. David Jensen, an Ontario Health spokesman, replied with a statement that did not address the questions specifically.
The province, he pointed out, has increased its testing capacity from 4,000 to almost 40,000 a day and continues to lead the country in both tests completed and daily testing capacity. The government has also invested over $ 1 billion to expand the lab network, secure supplies and hire staff.
On the decision not to restrict testing earlier, he wrote: “Earlier this year our broad range approach to testing helped us determine if and where COVID-19 was spreading. What we found was that it wasn’t widely circulating in any community. This was an important decision to target our resources to those experiencing symptoms, protect the most vulnerable and support outbreak investigations.”
For Riley, all of this feels a bit like déjà vu. “These things tend to be cyclical,” he said. “They repeat themselves. After it’s all over, he believes, there will be royal commissions and expert reports. “Everybody will be running around and coming up with ideas and plans,” he said, “and then 20 years from now, we’ll be in the same boat, with a different bug.”