The SARS-CoV-2 virus responsible for COVID-19 entered Quebec during the 2020 spring break period and may have been carried into the province by as few as 247 people, according to initial results from a study released on Sept. 21 by the Institut National de Santé Publique du Québec (INSPQ) and the McGill Genome Centre.
We asked Dr. Sandrine Moreira, Head of Genomics and Bioinformatics at the Institut, and member of the CanCOGeN Coordinating Committee, to explain the study and what it’s teaching us about the COVID-19 pandemic.
“Genomic epidemiology still has so much untapped potential for public health. I hope the analysis researchers in the CanCOGeN consortium are doing will demonstrate that this powerful tool should be added to the classic epidemiological toolbox for public health.” - Dr. Sandrine Moreira
What was your research team trying to learn about the spread of COVID-19 in Quebec?
Our goal was to understand where the first SARS-CoV-2 viruses that entered Quebec came from and test the hypothesis that the early Quebec spring break (starting on Feb. 29) had an influence on the epidemic.
We selected 734 samples from Feb. 25 (the date the first case appeared in Quebec) to April 1 (15 days after the Canadian borders were closed) and determined the genetic sequence for the SARS-CoV-2 virus in each. By testing samples within this timeframe — which also took the 1-14 day incubation period for COVID into account — we aimed to capture a clearer picture of the origins the virus that entered Quebec.
How does genetic sequencing show us the origins of a virus sample?
The genetic sequence of SARS-CoV-2, the virus responsible for the COVID-19 disease, slowly accumulates mutations over time. So, if we isolate and sequence a virus found Quebec, we can compare the pattern of its mutations to those from viruses isolated in other countries, helping us understand the virus’ origins. We did that with the genetic sequences of the SARS-CoV-2 viruses in our 734 samples, comparing them to virus sequences from around the world through an international database.
What are the most significant insights from these initial results?
The main result is that we detected 247 introductions of the virus to Quebec from outside the province. Compared to the number of virus introductions in other jurisdictions — in Massachusetts, for example, only 80 introductions were detected — this is significant.
Another key finding was where the viruses came from. While we detected some instances of the virus arriving from other Canadian provinces into Quebec, most introductions were from Europe, Latin America, the Caribbean and the U.S. This was expected, as we saw similar patterns elsewhere, and because these are popular spring break destinations. But what was not expected was how few cases (fewer than one per cent) came from China.
Another surprise was that when we compared the travel histories provided by patients to what was found by our phylogenetic analysis, we realized that people were bringing home viruses with unexpected origins. This was especially true for Quebecers traveling back from the Caribbean, who brought back SARS-CoV-2 viruses with origins in places like Italy, Germany and the Netherlands. The Caribbean was an international hub for virus exchange during the spring.
Why is this data important?
This genomic data analysis helps us better understand how the epidemic started in Quebec. It was the only way to confirm, with scientific evidence, the hypothesis proposed by epidemiologists early in the epidemic that spring break had a major influence on the spread of COVID-19 in Quebec.
We were also able to correct epidemiological information — often based on personal recollections and survey responses, which can be vague or not entirely accurate in painting a picture of the spread of the virus. We saw this with the example of spring break travellers returning from the Caribbean with viruses that had origins in other countries. Without genetic sequencing, this aspect of the travel history of the virus would not be accurately understood.
Genomic epidemiology still has so much untapped potential for public health. I hope the analysis researchers in the CanCOGeN consortium are doing will demonstrate that this powerful tool should be added to the classic epidemiological toolbox for public health.
What other potential does genomics hold when it comes to tackling major public health challenges?
Of course, there is great potential in epidemiology, but there are also lesser known applications that could have an enormous impact. One example is cases where patients have an infection that can’t be identified using classical tools. In cases like this, I’ve seen metagenomic sequencing, a powerful and complex analysis that sequences the entirety of a sample, offer patients a last chance at diagnosis. This type of sequencing is still not widely accessible, due to the complexity of the process and rarity of labs undertaking it.
At the public health lab in Quebec, we are developing these methods, as is the National Microbiology Lab in Winnipeg. Some labs in the U.S. and Europe are also doing it. We can be proud in Canada to have these tools in development for Canadians, and I think they will be more broadly accessible in the future.
The capacity-building aspect of the CanCOGeN initiative will help move this work forward. By building genomic capacity in Canada’s public health labs, CanCOGeN will help make tools like metagenomic analysis more broadly accessible in Canada.
What’s next for the research team working on this Quebec study?
Next, we will sequence more samples to get a more precise estimate of the number of introductions of the virus into Quebec. We will also look at which introductions led to the highest number of cases: the so-called “super-spreaders.” We will also look at what characteristics and trends within these cases are driving the epidemic, which is a very important question for public health.
By doing a joint analysis with colleagues from other provinces and with the National Microbiology lab, we hope to have a global picture for Canada which maps introductions of the virus in different parts of the country and characterizes more precisely the transmission of the virus between provinces.
You mentioned the importance of CanCOGeN’s capacity-building mandate to help researchers advance public health in Canada. In what other ways is CanCOGeN strengthening Canadian health research?
CanCOGeN funding makes studies like ours on SARS-CoV-2 possible. But this network is about more than just providing funds. It’s also bringing together academic researchers, genomics labs and epidemiologists from across the country to share expertise and facilitate data exchange. This is the kind of translational research we want to see more of in Canada.
In the news: First genetic sequencing of COVID in Quebec shows roots of outbreak (McGill Health e-News, September 21, 2020)
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.