How the Lab Responded to COVID-19
The Public Health Agency of Canada was, in many ways, born by the aftershocks of SARS-1,” says Guillaume Poliquin, MD, federal co-chair of the Canadian Public Health Laboratory Network (CPHLN) and acting director general of the National Microbiology Laboratory (NML). “There was always an awareness that coronaviruses that were pathogenic and a significant threat to public health could one day re-emerge.” Enter 2020.
Canada’s First COVID-19 Tests
The SARS-CoV-2 virus sequence was first published by Chinese researchers the weekend of January 10, 2020. As soon as Canadians had access to the sequence, the NML was able to compare the published data to generic assays the lab had developed earlier. At that point, the process of refining the tests began.
“Our first polymerase chain reaction [PCR] gene target test became functional on the 15th of January,” Poliquin notes. It took five days from sequence publishing to this first test. “Obviously, that first-generation test then went on for further refinement and development.”
This speedy response was partly due to the system’s earlier preparation, driven by the SARS (2003)1 and MERS (first in 2012 and then 2015)2 experiences.
Given the size of Canada’s population, over 37 million, it was immediately obvious that a central testing area in Winnipeg, Manitoba, was not nearly sufficient for the upcoming testing needs. The provincial health systems would have to be included.
“All the provinces and the National Microbiology Lab immediately knew that we would need a decentralized [approach], meaning all provinces would need to have [testing] capability,” adds Paul Van Caeseele, MD, provincial co-chair of the CPHLN and director of Cadham Provincial Laboratory in Manitoba.
At this point, the CPHLN became focused on making sure each province had access to the relevant information they needed to get their equipment up and running and the staff familiar with testing for the new virus.
It was a challenge to get the testing and capacity developed fast enough, according to Van Caeseele. “We were all racing to make sure we had good quality tests, and the science of the detection of the virus was still evolving. We didn’t even know which genetic target was the best.”
Bringing the Provinces on Board
Nevertheless, the move to provincial testing was fast. In early February, the Ontario Ministry of Health put out a call for hospital laboratories willing to perform COVID-19 testing. Typically, this type of testing is done at the public health laboratory, for epidemiological purposes and for data collection. This approach keeps things centralized and as cost-efficient as possible.
Such viral testing is usually not high volume, explains Christine Bruce, MHA, CHE, MLT and the new senior director of the Laboratory Medicine Program at the University Health Network (UHN). Before November, Bruce was the administrative director for microbiology in the shared lab of Mount Sinai Hospital, in Toronto, and the UHN.
Mount Sinai Hospital, part of Sinai Health, was among the first to raise its hand. “We had the ability. We had some equipment; we had a potential vendor to work with, who was showing early signs of having a test kit that they could bring to market fairly quickly with emergency use approval,” Bruce explains.
Mount Sinai and seven other hospital facilities obtained their licenses for the COVID-19 testing, making a total of nine labs (including Public Health) available for testing by PCR.
At first, the Mount Sinai team could perform 654 tests per day, the maximum capacity using their platform. At that point, they thought they were in a good spot, Bruce recalls. She remembers the team thinking that 600 tests should be plenty for them to manage. “And then we started getting calls.”
The lab received calls from other hospitals throughout Ontario. Public Health was running a turnaround time of five to seven days; the hospitals wanted to know if Bruce’s team could do better.
Bruce began committing blocks of capacity. She committed 150 tests per day for the Region of Peel. “Then Humber came forward. I held 50 tests a day, to try to spread the capacity and share it.”
Towards the end of March, Ontario Health brought in a more formalized structure to COVID-19 testing through an association with KPMG, a multinational professional services network. They formed a province-wide network to harmonize testing.
This more comprehensive approach allowed for better sharing of testing needs. For example, if Ottawa was short of materials and Mount Sinai had some to spare, they could share.
The need for testing continued to grow, along with the need for funding more machines, more supplies and more space. By mid- April, Mount Sinai was performing 2,800 tests per day, more than four times their earlier capacity. When the lab received an offer of new equipment from Wuhan, China, capacity grew again, reaching 8,000 tests per day. By early December, the lab was able to perform 17,000 tests per day.
Smaller Provinces, Different Needs
Ontario and Quebec have been the hardest hit provinces so far. The territories and Atlantic Canada have fared the best. For example, as of mid-December, New Brunswick had registered only 558 COVID-19 cases, compared with over 165,000 in Quebec and over 142,000 in Ontario. So, the testing needs in the lower-case provinces differ, too.
Testing began in New Brunswick in February, says Danielle McLennan, the provincial health care consultant in laboratory medicine for the New Brunswick Department of Health. In New Brunswick, COVID-19 testing is done at the provincial virology reference laboratory at the Dr. Georges-L.-Dumont University Hospital Centre in Moncton. “[W]e do not have a dedicated public health laboratory,” McLennan says. “Due to the provincial designation of the virology reference laboratory located at the hospital, they have been the conduit of information and collaboration with the NML on all matters relating to COVID-19 testing.”
Over the years, provinces and territories have adapted their pandemic plans based on previous outbreaks. “As good as the plans have been based on our previous experience, no one expected the unforeseen complications that arose relating to COVID-19 testing. International and national laboratories were all competing for the same required supplies to perform COVID-19 testing,” McLennan explains.
Turnaround times for test results vary according to demand. On average, turnaround time in New Brunswick is about 48 hours. The province noted there was an opportunity to improve the process by enhancing the transportation of COVID-19 samples. This modification, depending on testing volumes, has exponentially improved the process, McLennan pointed out. “The current NB laboratory information system provides minimal communication between each laboratory,” McLennan notes. “The NB Public Health Office requires consistent ongoing data collection. This can be a challenge without one unified laboratory information system.”
Bruce points out that many delays in Ontario’s turnaround time are due to manual data entry and different systems that don’t communicate with each other. Internally, the response time at Mount Sinai can be as low as nine hours, while externally, it is 14 hours. But the times can increase if tests need to be repeated due to an anomaly. And in other places, turnaround time is even longer because the sample must be taken, bagged, logged and then transported to the lab before the actual testing work can start.
Private Laboratories Enter the Field
As the need for increased COVID-19 testing continued, private laboratories stepped up as well. One company, Dynacare, now offers COVID-19 testing at labs in three provinces: Manitoba, Ontario and Quebec.
“We started off in Ontario because of a request to get the lab ready and to start offering the assay tests,” says Jenisa Naidoo, MD, chief scientific officer and vice-president of clinical development and quality assurance at Dynacare. The Manitoba government also requested testing. “It took a bit longer to launch there because we had to get the equipment.” Roll-out was faster in Ontario and Quebec because the company already had the equipment infrastructure. PCR testing went live in March. “We had the equipment to start off the first assays, and subsequently we acquired more equipment to expand testing.”
Staffing and sourcing the materials are also an issue for private clinics, just as in hospitals and provincial labs. Medical lab technologists had to learn about the new equipment, reagents, testing and methodology. “In Ontario, we now have the capacity of up to 8,000 tests,” Naidoo says. But that takes more staff not just to run the tests, but to handle the samples, too. “We were all tapping into the same pool for staff and they’re a hard pool to tap into. There aren’t many available.”
Private labs aren’t usually part of such testing, Naidoo adds. This increased the learning curve of their staff because this usually falls under the purview of public health.
However, staff was onboard right away and, according to Naidoo, have been exceptional. “There was truly that interest,” says Naidoo. “They wanted to be part of the solution, wanting to contribute, actually helping out.”
Staffing – Going Above and Beyond
Regardless of where the COVID-19 testing is done, there are some common issues that can cause problems along the testing chain.
Aside from the fragile supply chain, the labs cannot work without their staff. There’s no surplus of licensed medical technologists in the country, and the shortage may get worse as the average age rises and leads to an increase in retirements. However, lab directors and others are thrilled with the response of their staff and the level of professionalism since the pandemic began.
“Medical lab professionals have done a phenomenal job and have [performed] far beyond expectations in what they’ve managed to achieve this year,” Van Caeseele says. “It’s simply outstanding. It blows me away when I sit down and think about it.”
McLennan agrees, noting, “NB has done an amazing job.” She points out that laboratory professionals and support staff are used to a fast-paced environment in a 24/7 operation. But COVID-19 is different. This marathon of testing is into its first year, and it is unclear when there will be a reprieve. “I am humbled by their dedication and ongoing professionalism in this pandemic situation.”
Medical lab professionals have done a phenomenal job and have [performed] far beyond expectations in what they’ve managed to achieve this year. It’s simply outstanding. It blows me away when I sit down and think about it.
– Paul Van Caeseele, MD, provincial co-chair CPHLN and director, Cadham Provincial Laboratory in Manitoba
Medical lab technologists are used to working behind the scenes. Sitting at the bench, pipetting or doing other tasks, they may not feel like they are making as much of a difference as someone on the front lines. But Poliquin wants them to think otherwise. “All those results go back [so others can make an] informed decision. They can help someone avoid becoming infected. They help someone who is infected get the care they need. Every MLT in this [pandemic] response has made a material difference in the lives of Canadians.”
MARIJKE VROOMEN DURNING, RN
Special to CJMLS
- World Health Organization. “Severe Acute Respiratory Syndrome (SARS)” Accessed December 14, 2020. https://www.who.int/health-topics/severe-acute-respiratory-syndrome#tab=tab_1
- Centers for Disease Control and Prevention. “About MERS”. Updated August 2, 2019. Accessed December 14, 2020. https://www.cdc.gov/ coronavirus/mers/about/index.html