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From left to right: Dr. Lewis L. Tomalty, Dr. Henry Wong, Dr. Prameet Sheth, and Dr. Calvin Sjaarda

Queen's-KHSC labs leading the battle against COVID-19

(From left to right: Dr. Lewis L. Tomalty, Dr. Henry Wong, Dr. Prameet Sheth, and Dr. Calvin Sjaarda)

Dr. Prameet Sheth remembers this. The Queen’s researcher and clinical laboratory director at Kingston Health Sciences Centre (KHSC) recently looked up some planning documents from early in the pandemic – plans that forecast what his group’s workload would look like as COVID-19 spread.

They might have to process up to 20 COVID-19 tests a day, the plans said. Maybe even 30 to 50.

“And I open that up now and I’m like: Oh, you were such a naïve, young man. Those were good days!” the clinical microbiologist said.

The reality: “During the Omicron surge in December we did north of 1,200 tests in one day.” Some days even hit 1,500.

Dr. Sheth is an Assistant Professor in the Department of Pathology and Molecular Medicine at Queen’s University and the Director of Molecular Microbiology and Infectious Disease Sequencing at KHSC. The microbiology lab at the hospital is responsible for providing diagnosis of infectious diseases to people in Eastern Ontario – identifying viruses, bacteria, and fungi, and testing and reporting what drugs are appropriate for treatment.

But the pandemic changed everything, forcing the lab into a major transformation under difficult circumstances.

It has expanded to three shifts of staff, and about 35 full-time equivalent positions. COVID-19 testing, unknown before 2020, is now as much as half of the group’s work.

But diagnosing cases of the virus is now only half the story. This lab also has a major role in research and development – similar to an academic lab “tasked with developing and responding to emerging (and) changing epidemiology,” Dr. Sheth says.

Here’s the issue: PCR (polymerase chain reaction) testing is a method of identifying genes, but it takes different forms. The basic test looks at a small amount of genetic material and tells whether the patient is infected, but with no extra information beyond “positive” or “negative.”

But Ontario’s Ministry of Health announced in early 2021 that it needed more detail. It wanted to know what kind of virus was circulating and for that you need the “whole genome” of the virus – which means analysis of all the genes inside a virus in order to know which variants and sub-variants are present in Ontario, and in what proportions.

KHSC is one of four hospital labs in the province that do this. “They (the ministry) said: ‘Okay, we need to get this up and running in five weeks,’” Dr. Sheth recalls.

Dr. Sheth compares the period last spring to a military mobilization in time of crisis. “We went from doing 5,000 PCRs (tests) a year to doing 1,200 (or) 1,500 a day. I think that was an unsurmountable achievement that took people, training, developing and monitoring the supply chain that was increasingly difficult to do,” all the time maintaining a 24-hour turnaround for the tests.

“That in itself is an incredible feat.”

“We went up exponentially over a matter of days. We went from doing 50 a day to 100 to 200 to 400. There was no stopping us. And there was no room for error because the samples just kept coming.”

The drive required new equipment but also more staff. “We had to dig deep for people,” recruiting from the Queen’s community and also from St. Lawrence College.

But the disease threw curveballs at the researchers. Some staff became sick. Some had children who had to isolate at home. And the lab work can’t be done remotely. Dr. Sheth calls this period “very daunting.”

While expansion was the big achievement, a second was to set up a facility able to analyze the full genomes.

Dr. Lewis Tomalty, an Associate Professor in Queen’s Department of Pathology and Molecular Medicine, and KHSC’s Service Chief of Clinical Microbiology, recently found some old pandemic planning exercises from about 10 years ago. "There were some good ideas," he recalls, but no one back then came close to predicting the reality of COVID-19.

It is a sobering reminder that medical experts can't ever fully prepare for the future. When the demand for increased testing came, it was like "going from zero to 100, and then on to 1,000," he said.

As well, Kingston had to gear up while coordinating with other testing centres around Ontario, like Snowbird pilots who have to do difficult maneuvers while staying in formation. Somehow, it worked.

Still, about a year into the project he started to notice signs of exhaustion in the staff. All had to face the constant demand to go full-speed all the time. And because they work in a hospital setting, those with close contact with the virus had to spend 10 days off work, which threw a greater burden on others.

But he's proud today that no one backed off the pace.

Morale has remained high, Dr. Tomalty said, but there's also some frustration in dealing with the reality that some people in the community belittle the risk or doubt the value of what researchers and clinical workers are doing.

On top of all the testing work, all the findings had be reported to the province, Dr. Sheth said. “That means if you come into KHSC with clinical symptoms consistent with COVID-19, you get tested.” That goes into a provincial information system, “but with the emergence of different variants, the ministry wanted the whole-genome surveillance results to also go in as well.

“So now we monitor people that are hospitalized or in ICU using the whole genome information. Do they have Delta or Omicron? Because we’re looking at Omicron completely taking over, and we’re saying, okay, how do we plan for this? And is there going to be a new “variant” later?

Dr. Sheth is part of three labs that have worked closely with COVID-19. Two are service labs at KHSC: the Molecular Microbiology Laboratory – where he is joined by Dr. Tomalty – and the Infectious Disease Sequencing Lab. The KHSC lab team includes Drs. Henry Wong and Calvin Sjaarda – who are also heavily involved in Dr. Sheth’s lab in the Gastrointestinal Disease Research Unit (GIDRU) at Queen’s. That university research lab published one of the first genomic analysis of COVID-19 in Canada, conducted an Ontario-wide analysis of COVID-19, and co-studied the number of small-molecule chemicals in COVID-19 patients.

The future for this group looks just as busy and it’s likely to involve surveillance of patterns of respiratory viruses, influenza, and also the growing number of bacteria that are resistant to antibiotics. The World Health Organization has flagged these “superbugs” as a major threat, Dr. Sheth said, “so I think we’re likely going to expand our surveillance for other pathogens.

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