On Feb. 29, one of Ontario’s leading infectious disease doctors sent out an alert which boiled down to this: We are going to need help. Provincial labs needed help from private and hospital labs to process an expected daily onslaught of thousands of COVID-19 tests.

“Is there anybody else who has capacity to do testing or is willing to do testing?” is how Dr. Vanessa Allen describes her message.

When Allen, chief of Medical Microbiology at Public Health Ontario, sent out that request Ontario had only 11 confirmed cases and had tested roughly 1,000 people. To put that time in perspective, the Toronto Maple Leafs had just had a bounceback win after the loss to the “Zamboni goalie” David Ayres. The Toronto run of Lin-Manuel Miranda’s “Hamilton” musical was just getting started, and baseball’s spring training series was giving fans a sense they would soon be enjoying a game and a beer at packed ballparks.

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The approaching pandemic was not only far from the minds of most Ontario residents, it was also not battle stations at the Ontario government, where the focus was squarely on rotating teachers strikes. Sources in the lab sector, who asked not to be identified because they rely in part on government funding, have told the Star that it was generally thought that the well-funded provincial laboratory system should be able to handle a surge in testing.

But at the province’s state-of-the art lab complex on the top four floors of the MaRS building in downtown Toronto, there was a rapidly developing concern that sooner rather than later Ontario would require a capacity beyond its public health lab system to test for the virus that was disrupting other parts of the world. Private and hospital labs would be needed. Internationally, Italy had just reported 29 deaths and more than 1,000 confirmed cases and soon the virus would spread widely. In China, where it began, the tide had turned due to identification of cases through mass testing — to discover who and how many people had the virus — and social distancing. It was not yet a big story in the U.S.

In just two weeks the Public Health Ontario (PHO) labs in Toronto and satellite sites would have a backlog of 10,000 pending tests, which would not be cleared until the beginning of April. It was a public relations disaster, as negative headlines mounted and politicians struggled to explain the problem lab sources say was their own making.

Here’s how it all rolled out and what has happened to turn the tide.

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On Jan. 10, the “genome sequence” for COVID-19 was made publicly available. Around the world, including at the Ontario public health laboratories, microbiologists could now test for the virus. Ontario did its first test the next day, which was negative.

A key lesson taught by the late Dr. Don Low, the face of Canada's battle against SARS, was the importance of scientists talking to each other ?informally and often. (TORONTO STAR file photo)

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Allen, of PHO, was a medical resident during SARS. She was recruited into the public lab system by the late Dr. Don Low, for many the face of Canada’s battle against SARS. One lesson she learned from Low was the importance of informal and frequent conversations with others in her line of work. She and others were having those informal conversations starting in January. The SARS Commission itself had given a warning in 2004:

“The capacity of a laboratory system to respond to an outbreak of infectious disease must pre-exist any future outbreak, because it is impossible to create it during an outbreak,” states the first interim report of the SARS Commission.

But in Ontario, though there were improvements at PHO, there was no formal system — no boss or directing mind — for public, private and hospital lab scientists. Instead, infectious disease specialists at all types of labs were networking on their own (a formal system was just recently set up).

“There is no single oversight over all of that,” said Allen, reflecting on the situation in February and the first half of March. “We try to work together as best as we can but a lot of it is informal.”

It was in that context that Allen sent out a letter on Feb. 29, distributed by the ministry of health, to all potential lab testers.

“Dear Colleagues, in recognition of the need for expanded testing for COVID-19 virus (SARS-CoV-2), efforts are underway to co-ordinate and ramp up ASAP in Ontario,” Allen wrote in a letter widely distributed across the province. She wanted to know the capacity of labs, what equipment they used, who was interested in testing, and to make sure those who needed formal approval from the province got that process started.

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Some labs had already raised their hands, others responded to the letter. The two biggest laboratories — Dynacare and LifeLabs, which began doing COVID-19 tests the last week of March — have told the Star that, by the beginning of March, they were in conversations with the province to join the testing battle.

“The process to provide support (to Ontario) began when we received the capacity assessment (from the province) in early March,” said Dynacare’s Mark Bernhardt. “We were able to confirm our support and our ability to offer a high-quality test for COVID-19.”

LifeLabs spokesperson Chris Carson said his company took part in a provincial call on their testing capacity at the beginning of March. “That was the point where we started ramping up.”

Hospitals, including Mount Sinai Hospital, were also involved in the discussions.

The Star has asked the provincial health ministry why this was not started much earlier: perhaps in early February or even late January. The health ministry responded Friday evening with several general paragraphs describing what it is doing now, and ignoring the Star’s specific questions about why the Ontario government did not take an early, active leadership role on the laboratory issue.

“The Ministry of Health and Ontario Health have been working with Public Health Ontario, hospital, academic and private laboratories to aggressively ramp up testing capacity,” said a spokesperson for Ontario Health Minister and Deputy Premier Christine Elliott.

Absent provincial leadership, informal discussions continued.

Over the first two weeks of March, two things happened. A lot more swabs were taken each day from new patients with symptoms across Ontario — far too many for the PHO labs to process. And all of a sudden, there was a growing backlog of thousands of tests: more than 10,000. The backlog meant some people waited seven or more days for results, which was a public health danger and also meant that the public and leaders did not have an accurate picture of the pandemic in Ontario.

That’s because working flat out, Ontario’s public labs with the ability to do the tests could only process 3,000 tests a day.

“Three thousand molecular tests a day is a lot of tests for any lab,” said Allen. “There was a huge demand and the expectation was that a single lab could do that. In no jurisdiction has that been the case and been successful.”

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The public health labs added a third shift, so it could run a 24-hour testing program, seven days a week.

Testing for the virus in the lab is not a simple process. It requires specialized, and expensive, solutions called “reagents” and machinery to extract the DNA material from a nasal or throat swab, then seeing if it matches COVID-19. Allen’s lab was using one type of machine, the EasyMag by bioMerieux. Other labs had other types of machine. Roche and Abbott are two of the most popular machines.

Add to this the complication of time. Even though the province rushed through approval for the private and hospital labs to perform the COVID-19 tests — weeks instead of months — that further delayed help for the public lab system snowed under by tests.

At the beginning of April, Dynacare and LifeLabs were online had been running tests for roughly a week. Dynacare had run a maximum of 700 tests in one day. LifeLabs was up to 1,100 a day. Both companies expect to at least double their daily testing shortly. Two other private lab companies, Alpha Labs and BioTest Laboratories, will shortly begin testing. Other hospitals will soon join Mt. Sinai Hospital in testing.

Meanwhile, at PHO, their 3,000-a-day capacity will shortly be augmented by a new Roche machine which can run 4,000 tests a day. The province has said that by the third week of April, all labs involved in testing will be able to run almost 19,000 tests a day.

But there is a hitch. Each machine takes a different reagent — the chemicals used to extract the DNA. You cannot use the reagent for one machine in another machine. The reagent for some machines is more difficult to acquire than others because of demand throughout the world. Roche, in particular, is in demand. It is quite likely that some machines will sit idle while others hum along, all because a machine has run out of the reagent chemicals.

At PHO, Allen said that the new formal system for co-ordinating labs — informally called the “COVID testing table” — is a “silver lining to this.”

The testing backlog is now cleared, something Allen said was difficult for all concerned.

“It was very disappointing for us, and I think particularly heartbreaking for me, because we are committed to the health of the people we serve,” said Allen. “Our staff are working so hard to maximize capacity and so it has been a very difficult week, I know, for the recipients of those test results — and also for our staff, given what we see as a primary responsibility to serve the public.”