Canada’s COVID-19 Variant Hunters

Variants of concern have dominated international headlines during the COVID-19 pandemic. A small team of Government of Canada employees, called Genomics Liaison Technical Officers (GLTOs), have been instrumental to Canada’s identification and tracking of the variants. These experts are working directly in provincial public health labs doing whole genome sequencing to inform local and national responses to the evolving threat.

As the SARS-CoV-2 virus continues to circulate and cause infection, it provides opportunities for mutations to occur and for new variants to develop. This creates a dynamic public health concern that places importance on monitoring how the virus is evolving. The ability to scrutinize genetic mutations has revolutionized the way scientists battle viruses, including those at the Public Health Agency of Canada’s National Microbiology Laboratory (NML).

When the first variant of concern emerged in December 2020, genomic sequencing and bioinformatics – the skillset required to crunch sequencing data – were limited resources in Canada. Recognizing the capacity shortfalls, the Government of Canada dedicated $53 million towards a Variant of Concern Strategy to rapidly scale up sequencing and scientific efforts to detect known and emerging COVID-19 virus variants including Omicron.

Boots on the ground

To quickly build national sequencing capacity, the NML worked with provincial and genomic public health networks to identify regional needs in each province. In addition to buying lab supplies, the NML worked with provincial labs to hire sequencing and bioinformatic experts, who are federal boots on the ground working jointly with their provincial counterparts. They are dedicated resources to boost sequencing and scientific capacity on the front lines where, how, and when it is needed most to battle variants. (Read more about NML’s role in boosting national COVID-19 testing capacity here.)

The on-site sequencing capacity meant samples did not need to be shipped across the country to be sequenced. Prior to this program, some provinces did not have any genomic sequencing capacity for public health surveillance. In other provinces previously, laboratory personnel were re-deployed to diagnose active infections during the peak of COVID-19 waves.

Catherine Yoshida leads the GLTO team, informally referred to as ‘Gelatos’, along with three Scientific Project Coordinators, Dr. Andrea Tyler, Dr. Genevieve Labbe, and Dr. Ana Duggan.

She explains how having dedicated genomic experts on-site at provincial labs results in increased capacity so more samples are sequenced, with the ability to turn around results faster than ever before.

“It took five days from the time we received the first signal of a concerning new variant from the international scientific community for Omicron to be identified, and for Canada to confirm our first cases, resulting in swift public health action,” says Ms. Yoshida. “The speed with which that happened was previously unheard of and it speaks volumes to the capacity and network that we are building.”

Creating paths of communication

It’s not only the quick lab results that have proven critical but also the relationships formed with the provincial labs. Dr. Kara Loos, a GLTO working at the Roy Romanow Provincial Laboratory in Regina, explains that part of the officers’ job is to create paths of communication and knowledge sharing.

“Every laboratory is different, and we help translate between the provincial and federal labs. Also, we have established a network where we can share information with other team members and create efficiencies through shared training processes,” says Dr. Loos.

The presence of the GLTOs also meant that the lab could divert resources to diagnostics during the Delta and Omicron waves while maintaining its ability to conduct genomic surveillance.

“The federal scientists who joined our team have brought with them valuable expertise and are contributing to the sustainability of our province’s genomic surveillance program,” says Dr. Jessica Minion, provincial clinical lead for Public Health in Laboratory Medicine at the Roy Romanow Provincial Laboratory in Regina.

Pierre Lyons, a GLTO who works in Moncton, New Brunswick, is tying the linkages between the provincial labs and local epidemiologists by working with them directly, developing an integrated system in New Brunswick. He generates sequencing analyses that he shares with epidemiologists to help inform their contact tracing, drastically shortening their time for outbreak investigations, which has helped to contain outbreaks.

Genomic surveillance beyond COVID-19

Ms. Yoshida says they aim to leverage the genomic surveillance capacity developed during COVID-19 to enhance and strengthen surveillance for other infectious diseases; for example, by bringing genomics into routine surveillance for tuberculosis or antimicrobial resistant pathogens.

“COVID-19 enabled us to explore this option at a dramatically increased scale. It identified the need that goes beyond what we had the capacity to support before,” says Ms. Yoshida.

Going forward, the NML is developing a training program for both genomics and bioinformatics to maintain capacity and competencies in this area.

“All of this will build the expertise for genomics and bioinformatics within Canada. It’s not only finding the talent, but continuing to maintain and develop that talent domestically, and keep up with a highly innovative area where the science is moving quickly and the technology continues to evolve.” says Ms. Yoshida.