On March 10, 2020, Sunnybrook microbiologists Dr. Samira Mubareka and Dr. Rob Kozak were part of a team who isolated SARS-CoV-2, the virus responsible for the COVID-19 pandemic. We spoke to these two researchers about how they did it and what isolating the virus means for science and the future of the outbreak.
Q: What does it mean, isolating the SARS-CoV-2 virus?
Dr. Samira Mubareka: Essentially, isolating a virus means it has been cultured or propagated from an original sample, in this case from clinical specimens collected from patients presenting with signs and symptoms of COVID-19. This work was done in a high-containment lab, because SARSCoV- 2 is a higher risk virus compared to some of the more common ones we work with, such as influenza virus.
Dr. Rob Kozak: The nice part about virus isolation is that the virus does most of the hard work. What we do is take some liquid media from a tube that has the patient swab – in this case, from a nasal swab – and put it onto a cell line. These are basically cells used by research labs that are continuously replicating. The virus needs cells to grow. Then we just wait and look for the cytopathic effect, where the virus is breaking apart or killing the cell, and we can visualize this with a microscope. Then, you confirm the virus’s presence with a molecular test.
The hardest part on our side was just the patience. You’re sitting there biting your nails, waiting for it to work.
Q: What can you do now with the isolated virus?
Dr. Mubareka: Now we have a tool we can use to pursue other research. We can look at the efficacy of antivirals or vaccines, or how good diagnostic tests are. You can’t really do any of that if you don’t have the virus. Viruses are like small molecular machines, and it is essential to understand how all parts of the virus interact with each other and with parts of the host cell.
Dr. Kozak: The more we understand about the virus, the more we understand about how it causes disease. If we better characterize how the virus replicates, we can figure out points in its life cycle that antivirals could target. We also need to have the virus if we’re going to do vaccine-challenge experiments. That’s where you vaccinate a preclinical model and then you wait for it to build up its immune response, then you give it the SARS-CoV-2 and see if the vaccine has provided protection.
Dr. Mubareka: One of the other things we’re focusing on quite a bit now is doing whole genome sequencing of the virus.
Q: Why is it important to genome sequence the virus?
Dr. Mubareka: We know the virus is passing from person to person, but we don’t know all the details about how the virus might change during that process. We need to know what the virus looks like right now for a couple of reasons. For one, once we start vaccinating people, we don’t know how the genetic code of the virus might change, so genome sequencing is important for surveillance to detect changes that may affect vaccine efficacy.
It is also possible that there are some subtle differences in parts of the virus that trigger different antibody responses. So if, for example, there are some differences in Canadian viruses versus ones from Europe or Iran, it would be good to be able to make sure that a vaccine will neutralize the virus that’s in circulation in each of those places. It is also key to understanding viral transmission and to investigate outbreaks.
Q: Tell us a bit about the collaborations Sunnybrook is involved in.
Dr. Kozak: We had a lot of support and advice from a number of different international collaborators. I reached out to colleagues in China and Australia who were kind enough to share tips and tricks, which I think was incredibly helpful.
Dr. Mubareka: We also worked with in collaboration with Dr. Arinjay Banerjee from McMaster University. He brought quite a bit of expertise to the table, because he’d done his PhD on Middle East respiratory syndrome-related coronavirus (MERS). Since isolating the virus, we’ve sent it to a number of other containment labs in Hamilton, London, Montreal, and we anticipate sending it to Vancouver and Calgary. We’ve also shared RNA from the virus and inactivated virus with other research groups, including the University of Toronto research community.
Q: This is an unprecedented event. What are you learning from these challenging circumstances?
Dr. Kozak: This pandemic has highlighted that we need vaccines and therapeutics as quickly as possible, and it is difficult to be fully prepared for the unknown, but we can try to improve our chances. For example, you can support research to develop antivirals that work against entire groups of viruses, [such as] all coronaviruses, not just SARS-CoV-2. Then, when you have another emerging virus from that group, you have some potential options on the shelf.
Dr. Mubareka: RNA viruses cause the majority of emerging and zoonotic viral pathogens [viruses that pass from animal to human], including Ebola virus, Zika virus, MERS and now SARS-CoV-2. The challenge, not only in Toronto but provincially and nationally, is that there are few RNA virologists or centres of excellence in RNA virology.
One of the reasons we were able to act quickly early in the outbreak was that we had existing relationships and collaborations that could be leveraged. Going forward, we need to build programs based on what we have established over the past few months; this will develop resilience for future emerging viruses.
Dr. Kozak: The support for research, and all aspects of pandemic preparedness, must continue after COVID-19 is beat. We have to stop thinking of research and pandemic preparedness as a luxury. The cost of prevention is a lot less than the cost of response.
Q: Why have you both chosen to work in this area of research?
Dr. Mubareka: My interest in microbiology stems from my interest in infectious disease. What I find intriguing about infectious diseases is that it matters what happens on the other side of the world. There are so many variables – from a macroscopic population level all the way down to small changes in one part of the virus [that can] change the disease it causes, how easily it’s transmitted or which hosts it infects.
Dr. Kozak: My mom was a virologist. As a kid, I read a lot of books like The Hot Zone, which is the story of the Ebola outbreak in Reston, VA. Between my mom’s interest in viruses and these books that I read, I was kind of hooked on microbiology. I also share some of the same thoughts as Dr. Mubareka. The more you learn about viruses, the more you start to see that we’re all kind of one big community, and the things that happen in one person’s backyard absolutely affect what happens somewhere else.