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Understanding the impact of COVID-19 on Black Canadians

Friday, February 26, 2021

Q&A with Dr. Upton Allen

Dr. Upton Allen

Dr. Upton Allen, head of the Division of Infectious Diseases at The Hospital for Sick Children in Toronto, is on a mission to ensure Black Canadians aren’t left behind in the race to fight COVID-19. He is leading a large-scale study on COVID-19 prevalence and risk factors among Black communities in Canada, which will help inform public health response with the goal of developing more robust and equitable safety measures and supports for the affected persons. Another current project looks at genetic susceptibility to COVID-19 and related outcomes.

COVID-19 shows significant variability among communities and individuals, ranging from an unnoticed infection in asymptomatic people to a lethal disease. That’s why researchers across the country, such as Dr. Allen, are working together and collaborating with the Canadian COVID Genomics Network (CanCOGeN)’s HostSeq initiative through independent studies that will help us understand differences in patient outcomes.

As Canada’s national platform for genome sequencing and analysis, CGEn is leading HostSeq and working to develop regional, national and international links to ensure no Canadians are overlooked in the national response to COVID-19. While delivering on its commitment to sequence the genomes of 10,000 Canadians affected by COVID-19, HostSeq also aims to build a national databank of genetic and clinical information that is representative of Canada’s diverse population. 

We asked Dr. Allen about the studies he is leading, the importance of diversity in clinical studies and how the data generated through HostSeq can help improve COVID-19 health responses for Black Canadians.


“It’s extremely important for Black Canadians to be directly represented in studies to make sure the data we obtain are directly applicable to them. This is a much more relevant  approach than using data from other populations and then extrapolating it back to them.”


You are a strong advocate for more diversity within clinical trials and are currently leading a study that focuses on Black Canadians. Can you describe your work in this area and the importance of representation in clinical studies?

Racialized communities are disproportionately affected by COVID-19. Toronto Public Health data from August showed that Black people make up nine per cent of the population but more than 20 per cent of COVID-19 cases. We wanted to get a better understanding of why this was happening.

We want to examine the extent to which COVID-19 had penetrated into the community and the socioeconomic, demographic and medical factors that might be associated with an increased likelihood of somebody having COVID-19. The social determinants of health are major risk factors. Data have emerged, and are still emerging, that show that the social determinants of health — things like income, where you live and access to health services — influence who gets infected and who has good and bad outcomes.

For our seroprevalence [the level of a pathogen in a population] study, we began engaging study participants in the summer with the goal of including about 2,000 Black Canadians. We will also include up to 1,000 others from specific postal codes to use as a comparison, because in some communities, the risk factors likely cross racial and ethnic lines.

How important is trust and community engagement in your work?

It’s absolutely critical. The Black community definitely has issues of trust in relation to their treatment in the healthcare system. There’s no question about that. Even for me as a Black physician working with a community, the first thing that the community sees is a member of the healthcare system. One has to recognize that initial barrier has to be overcome. It requires a long process of carefully and closely working with community groups to build trust.

In preparation for our study, we worked with the community for about four months to set up an advisory group. We meet regularly with them to get feedback, hear what’s going on at the community level and update them on our process. For example, as our preliminary data emerges, we share it with the community before it’s even presented to the wider public.

How is information from host genome sequencing helping you achieve your goals and contribute to Canada’s COVID response?

Our seroprevalence project has the potential to facilitate another of our studies aimed at genetic susceptibility (genMARK study). The latter links with the HostSeq initiative. Having the genomes of individuals infected by the virus will help us understand the individual variability in patient outcomes. The genMARK study looks at genetics to determine why people in our study got COVID-19 in the first place and perhaps, depending on the clinical severity, why they had severe COVID-19. Genome sequencing and analysis from HostSeq will help with generating the immunogenetic data, which potentially could be linked with the social determinants data to get a better understanding of what’s going on.

By identifying who is at risk, we will be better able to support prevention strategies. Having a funding process that allows us to rapidly generate data targeted to the needs of unique populations’ is key.

How will this work help in the future? Could it help with vaccine uptake?

Our community engagement approach is a template that can be built on for ongoing cooperation. We want to continue working with the communities to provide useful information that improves the lives of individuals and strengthens the community as a whole. For example, the connections we’ve built with local Community Health Centres enable information exchange that connects our work to the larger community. Engaging these close contacts and empowering them with the data we’re collecting could help with educational efforts around vaccine uptake in the immediate future.


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.