Dr. Caroline Colijn is a Canada 150 Research Chair in Mathematics for Evolution, Infection and Public Health in SFU’s Department of Mathematics. She leads the MAGPIE Research Group (Mathematical Genomics and Prediction in Infection and Evolution) which carries out research that intersects mathematics, epidemiology and the evolution of pathogens.
Throughout the pandemic, Colijn and her team have worked closely with the B.C. Centre for Disease Control, Genome BC, the Public Health Agency of Canada and others to develop mathematical models to inform the COVID-19 response. Her research articles have been cited and shared thousands of times, and she’s been a source of clarity and information for the general public in Canadian and international media.
One of her most-cited articles this year is The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic. Prepared in collaboration with scientists from across Canada, the article describes the emergence of variants of concern and the changing evolutionary selection impacting the SARS-CoV-2 virus.
Colijn recently discussed her modelling methods, while reflecting on her experiences over the past 18 months.
When were you first contacted to use your expertise to model the trajectory of the emerging COVID-19 virus?
I have been working in the area of infectious disease modelling since 2006, on various infections including tuberculosis and Strep. pneumoniae. That got me interested in the evolution of infectious disease pathogens and how to use pathogen sequencing data for infections to understand and hopefully prevent transmission. So I was already involved in developing dynamic models looking at how infections spread and the impact of evolution.
Before the pandemic was declared, there were already papers on the “novel coronavirus” on bioRxiv [pronounced bio-archive server] – a preprint repository for the biological sciences. I decided to host a hack-a-thon at SFU where we got into the early data and early papers. It was February 2020 and this was just hitting the news, but had not been declared a pandemic. It generated a lot of interest from different groups.
A representative from the BC Centre for Disease Control (BCCDC) attended the hack-a-thon, and spoke about what information would be helpful in the interest of public health. We organized teams around those questions. From there, we formed a modelling collaboration, and started to work with the BCCDC, and later with the Public Health Agency of Canada (PHAC).
What is pandemic modelling and how does it work?
Basically, our models take what we understand about COVID-19 and synthesize that information into a representation of the system to which we can then ask questions. We take relevant knowledge – things like transmission rates, vaccine efficacy, how long infections last – and build a model so that we can test our assumptions and interrogate against what we know. So we ask things like, where is this going? What if we continue on this path? What happens if we did something else?
Models are a very safe way to run an experiment that we can’t run in the real world. For example, using a model we can predict what might happen if we halve or double transmissions. Models are a toolkit of the knowledge we have that allows us to explore what happens when we change things. They also help us look for gaps in data and knowledge.
How does genetic sequencing help us understand COVID-19?
We can read the RNA of a pathogen and define what it is as a virus – and this virus has several variants –the original novel coronavirus strain, the Alpha, Beta, the Delta variants. The virus is changing, as all organisms do as they undergo diversification and selection. That evolution is going to continue. The Alpha variant was more transmissible and had higher severity, causing more hospitalizations. Delta was again more transmissible, and more severe than Alpha.
By sequencing the viruses, we can understand not only what variant they are, but we can get a high resolution picture of transmission. If two individuals have incredibly closely related viruses, they might have infected each other. Part of our research for years has been using sequencing information to understand transmission dynamics. For this virus we are looking at whether we can detect differences in the subtypes as to how fast they transmit. We’re also looking at how the virus is moving geographically using virus sequences, and we’re looking at how linked data on immunization, on severity and transmission can help us to better understand how the virus is evolving.
What types of variants are we likely to see over the next year?
When we saw the Alpha variant emerge in the U.K., it was at a time when no one was vaccinated, back in the fall of 2020, before vaccines had been approved. In a population like that, a more transmissible virus is going to have an advantage. Right now, that selection is different because most people are immunized. In places like Canada, in a highly immunized population, evolution will start to favour variants that can get into people who have been vaccinated. However, our immunity is complex and broad and the vaccines confer strong immunity. What we do have to look out for is continued evolution around both immune escape and transmission. For example, Delta emerged in a population with very little immunization, but we need to look out for new strains of the virus that are better able to get into immunized people. That may not happen and we hope it doesn’t, but it’s something we want to monitor.
COVID-19 is going to be with us for a while. Do you think we will ever be able to relax our control measures – or do you see some form of mitigation such as vaccine passports, masks, distancing well into the future?
I don’t think we will be able to eradicate COVID – it’s all over the world and it’s also in animal populations. It will be with us, but I think we will get enough immunity, largely through vaccination, to be able to re-open and have a “new normal.” We will just have to settle upon the mitigation measures that we are willing to accept and maintain indefinitely. That could include things like hand washing, good ventilation, ongoing testing, not going to work or school if we are sick. We will hopefully be able to settle upon living with COVID in a way that it does not challenge our health care systems, but whether COVID levels stay low enough for that will depend on a lot of unknowns.
It’s been quite a busy time for you as a researcher, policy advisor and media expert – can you comment on your experience over the past 18 months?
It is sometimes hard to know as academics what impact we have. We can’t rerun the world without our work in it. For example, my group and I were one of the voices – among many – arguing for vaccination of essential and frontline workers in Ontario and B.C. early on in the program. I don’t know that we had a direct impact in making that happen, but I am glad that it did.
I’ve done a lot of work in the media and I enjoy it. I think as publicly funded scientists we have a role to play when the public needs information. We need Canadian voices, specific to our context, our cultures and the needs of our communities. I have appreciated contributing to that and I hope my body of work has helped and has had some impact.