Q&A with Dr. Matthew Croxen
Increasing Canada’s capacity for genomic sequencing and data sharing has been essential to tracking the evolution of SARS-CoV-2 and informing Canada’s response to COVID-19. We asked Dr. Matthew Croxen, Co-Chair of the Canadian COVID-19 Genomics Network (CanCOGeN)’s Capacity Building Working Group, how sequencing has changed over the course of the pandemic and what it means for Canadians.
Dr. Croxen is Public Health Genomics Lead for Alberta Precision Laboratories and an Assistant Professor in the University of Alberta’s Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry.
“I think there’s now more of a shift and a realization that genomics is the next piece in the pathogen surveillance picture for public health labs…The capacity we’ve built through CanCOGeN, and generally throughout the pandemic, can be extended to other infectious diseases such as foodborne pathogens, influenza, tuberculosis and antimicrobial resistance bacteria.”
– Dr. Matthew Croxen
Can you describe your work within CanCOGeN?
Over the last two years we’ve helped build genomic sequencing capacity—from providing funding for sequencing-related equipment to training personnel—here in Alberta and across Canada so we can continue to address SARS-CoV-2 variants and future pandemics. Early in the pandemic, the most urgent need was to bolster sequencing capacity at the provincial and territorial Canadian Public Health Laboratories. We also recognized that certain hospitals required a small amount of sequence capacity.
How has Alberta’s sequencing capacity changed throughout the pandemic?
In the beginning of the pandemic we had a little bit of sequencing capacity, but not a lot. We initially had one technologist working to figure out the laboratory methodology and get used to sequencing a novel RNA virus that we knew very little about. At first, we only had sequencing capacity in Edmonton. Now, we can sequence at sites in Calgary and Edmonton, which are outfitted with various sequencers. We also have more people trained at both sites and are sequencing about 800 to 1,000 SARS-CoV-2 genomes a week with that capacity.
How has genomics sequencing informed Alberta’s public health response to COVID-19?
We were able to provide rapid information on the virus and new variants of concern. Sequencing gives us a detailed look at the genetic makeup of the virus, which enables us to spot differences in the mutational profile of a given sample. This allows us to determine whether a SARS-CoV-2 virus is a variant of concern. This has really helped inform public health, because we can rapidly tell what variants are circulating. When the Alpha variant (B. 1. 1. 7) was first announced in the U.K., our sequencing gave us the ability to look for the mutation profile in SARS-CoV-2 genomes collected in Canada, confirming the presence of Alpha circulating here.
In Alberta, we’ve also coupled the sequencing with a rapid variant screen assay. This is a quick test, which can detect the various variants of concern. When Omicron first started to hit the news, Delta was still the dominant variant of concern circulating in Canada. We were able to use this rapid screening to identify Delta variants so we could focus our sequencing efforts on non-Delta variants, which helped us quickly identify the presence of Omicron in Alberta.
The Canadian VirusSeq Data Portal was launched in April 2021 to facilitate SARS-CoV-2 data sharing across Canada and support researchers tackling future public health challenges. How are researchers using this new tool?
Alberta and most provinces contribute to the Canadian VirusSeq Data Portal. It’s an alternative to another public archive called GISAID, which houses millions of global SARS-CoV-2 genomes. The Canadian VirusSeq Data Portal only hosts Canadian SARS-CoV-2 genomes. It’s a kind of a one-stop shop to access Canadian sequence data, so you don’t have to sort through all the global SARS-CoV-2 genomes on the GISAID portal.
In terms of what researchers are doing, the VirusSeq Portal is public, so they have open access to the data. There are researchers across Canada who are looking at some of the different lineages of SARS-CoV-2 and trying to model the fitness and growth rates of particular variants in various provinces. A few days ago, a researcher reached out to me with a question about the frequency of a certain mutation in their target gene. I was able to quickly download all 180,000 Canadian genomes from the VirusSeq Portal in a couple of hours and let the research know the distribution of mutations in that gene from the SARS-CoV-2 viruses circulating in Canada since the beginning of the pandemic. VirusSeq is a powerful tool to answer researchers’ questions, providing quick and open access to the Canadian context of the SARS-CoV-2 pandemic.
Will CanCOGeN’s activities and investments over the last two years have an impact beyond the current pandemic?
I think there’s now more of a shift and a realization that genomics is the next piece in the pathogen surveillance picture for public health labs. Genome sequencing provides a lot more information than traditional typing methods used for pathogen surveillance, which is often limited to a small portion of the genome – and usually does not involve any sequencing whatsoever. The capacity we’ve built through CanCOGeN, and generally throughout the pandemic, can be extended to other infectious diseases such as foodborne pathogens, influenza, tuberculosis and antimicrobial resistance bacteria. That was an important aspect of the work of the CanCOGeN Capacity Building Working Group: building capacity for SARS-CoV-2, but also lay the foundation for other pathogen surveillance. Many of the public health labs across Canada now have the capacity to take on different surveillance priorities for other priority infectious diseases. We’ll have more tools and abilities to do better infectious disease surveillance, but also in a collaborative manner as we did with SARS-CoV-2.
We’re proud of what we’ve done in response to the COVID-19 challenge, but there’s a lot of work and big questions ahead. How do we keep up this momentum? How do we make it sustainable and continue working together? The CanCOGeN capacity building funding has helped provide the foundational pieces to address these challenges and has set Canadian public health laboratories up for future success.
The Canadian COVID-19 Genomics Network (CanCOGeN) is on a mission to respond to COVID-19 by generating accessible and usable data from viral and host genomes to inform public health and policy decisions, and guide treatment and vaccine development. This pan-Canadian consortium is led by Genome Canada, in partnership with six regional Genome Centres, the National Microbiology Lab and provincial public health labs, genome sequencing centres (through CGEn), hospitals, academia and industry across the country.
Photo: COVID-19 testing at the lab at Calgary’s South Health Campus (Alberta Precision Laboratories)