Natalie Prystajecky
Program Head, Environmental Microbiology & Molecular and Microbial Genomics Programs - BC Centre for Disease Control

COVID-19 Research: Genomics, Collaboration and Funding

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COVID-19 Research: Genomics, Collaboration and Funding 

Takeaways

  1. Emerging technologies like genomics and next-generation sequencing are providing the research community with data-driven science to track the spread of COVID-19 and develop diagnostic tools.
  2. The Canadian government and funding agencies have shown their commitment to the research community by funding diverse research opportunities related to COVID-19.
  3. Although the Canadian media is covering the number of COVID-19 tests taking place each day, it should also focus on testing methods and how to use the data that is collected.

Action

The Canadian government and funding authorities should continue to invest in public health, scientific technologies and research to prepare Canada for future outbreaks. The innovations Canadian researchers are currently relying on—in genomics, informatics and applied sciences—are the result of sustained investments in the research community. These investments must continue to ensure Canada has a strong research community and public health function.


How Are Emerging Technologies Being Used to Fight COVID-19?  

A good example of Canadian leadership in using technologies to deal with this outbreak is the field of genomics. 

Genomics is a perfect example of an emerging technology that is helping with this outbreak specifically. If you look at SARS from 2003, it took about six months to generate a complete genome of that virus. With this outbreak, it took about two weeks. The World Health Organization (WHO) first became aware of a pneumonia of unknown origin at the end of December. By January 11, the first genome was publicly released.  

If you look at SARS from 2003, it took about six months to generate a complete genome of that virus. With this outbreak, it took about two weeks.

This was really important for a few reasons. The first was that it allowed us to develop diagnostic tools or tests to determine whether or not somebody had COVID-19. But it also set the precedent for using genomics to steady this outbreak and release the data publicly and quickly. We are using technology to understand how the disease is spreading here in Canada and in British Columbia. That could not have been done without emerging technologies such as next-generation sequencing.  

I can really speak more about the testing technologies as opposed to the informatics technologies—but people have been talking about using machine learning and AI to crunch the data. I think that is one of the things that is coming out of this outbreak—just how much data has been made available quickly, and how that is quite different from previous outbreaks. Whether it is an entire genome of the virus, the number of tests performed, or creating projective models, it is clear that we are living in a data-rich environment and more advanced tools are certainly needed. 


What is Genome Sequencing and What Role Does It Play in Fighting COVID-19?  

Genome sequencing is basically sequencing the entire genetic code of a microorganism. In this case, we would sequence through all of the RNA that makes up COVID-19. We are doing this for a few reasons.  

In the very beginning, genomics was used to ascertain: what was this organism that was causing this unknown pneumonia? After that, it was used to identify diagnostic methods to detect the organism. We see the number of different genomes and determine where there are staple sequences that we can use for diagnosis. Now we are at the point where we are using genomic sequences to understand transmission. Do case A and case B—which may not be related—have identical sequences? What does that mean?  

For example, in our scenario, from the very beginning of the outbreak you could really link people’s travel history to the genetic sequence of the virus if they were carrying it. It really helped us understand how the virus was spreading and where the virus was coming from. Genomics provides so many different types of data it can even help us understand how a vaccine might work—whether or not we can expect to have vaccine boosters, new strains or new vaccines every year. What we are seeing with this virus so far, is that it is pretty stable—it does not change a lot—and we do not expect it in combination like we do with influenza. It might be that a vaccine that is produced might provide protection for quite some time, and we can predict that from the genome sequences.  

It might be that a vaccine that is produced might provide protection for quite some time, and we can predict that from the genome sequences.  

Likewise, we can understand what some of the therapeutic interventions might be—what types of drugs might work best against the virus—just based on the genetic sequence. Genome sequencing helps us in many realms of understanding the disease and the impacts it has on patients.  


What Are Your Current Research Priorities?  

Everything is COVID-19 right now and that really is our priority. The diagnostics, the research—everything is focused on COVID-19 because our main priority is to fight this disease.  

In general, what I was doing prior to COVID-19 was really focusing on operationalization of genomics. When we are talking about genomics, that is sequencing the entire genome of bacteria or a virus. In this case, we have been using genomics to study foodborne illnesses, which I am very interested in. That is being able to find a genetic sequence—a pathogen that is in the human and in the food they consume—and matching them to say that, in fact, this is where they became sick. That really helps in how we investigate outbreaks and what measures we can put into place to prevent future outbreaks. 

We are doing similar things for COVID-19—being able to sequence the entire genome to understand whether or not two cases are related to one another. That is really important technology, and it is actually going to transform the way we do microbiology. But of course, there is a big learning curve for that. We are trying to find a way to best implement it—it is expensive, it requires new training and new technologies—but we really want to be able to understand how we can transform the way we do public health in the future.  


What Lessons Have We Learned from Previous Epidemics That Have Shaped Our Research Response to COVID-19?  

For me, this is the first pandemic I have been involved in. I think that there is certainly a history of different epidemics and pandemics that have affected Canada. There was Ebola—which did not come to Canada—but we were working on preparedness for that. We had H1N1 in 2009, and then SARS in 2003. The previous pandemics really shaped how we respond to public health emergencies and how we integrate the research community. That is because it is more than the frontline physicians and public health workers that need to be involved in this. There is certainly a research domain that can help accelerate our response. Canada has really learned from those previous experiences.  

The previous pandemics really shaped how we respond to public health emergencies and how we integrate the research community.

What you see from these research calls—from Genome BCGenome Canada, and the CIHR—is that people really want to invest in research, and that can happen at a really fast pace. Making that funding available quickly allows us to accelerate the work that we do. The turnaround times for some of those funding opportunities is sometimes less than a week, and if you look on the Genome BC or CIHR website, you will see that this funding is happening here in Canada. There is everything from therapy and genomics, to vaccine development, to modelling how the disease is progressing and its social impacts. The breadth and the number of researchers that have been funded really shows Canada’s research capacity and the investment from our government and funding agencies to support that.  


How Are Canadian and International Researchers Collaborating to Fight COVID-19?  

Collaboration is key for fighting this disease and you will see that happening on multiple scales—whether it is the level of trade, sharing PPE, or being able to work together in this crisis.  

I will give you a really good example of how collaboration has occurred. The first QPCR or quantitative PCR acid that is used for diagnosis was released by the World Health Organization after one researcher uploaded their method. That was uploaded in mid-January, and we are now using part of that method. In the previous era, somebody might have waited to publish that into the peer-review literature to receive kudos—but that is not what is happening here. What is happening is that people are releasing their methods without going through peer-review. They are making things available so that we do not have to wait two or three months to have that data. We emailed those researchers, and that collaboration allowed us to produce a good product really quickly.  

This is not a time for glory, it is a time for sharing and collaboration. 

Likewise, we developed our own method and shared it with researchers across Canada and at different sites in British Columbia. This is not a time for glory, it is a time for sharing and collaboration. We have to help each other advance our methods and sharing data is really important in method development. I do not think we would be where we are today with respect to testing capacity if we had not collaborated with the international community.  

One of the challenges with collaboration is that things are just changing so quickly—within days, a new project is emerging, and we need to get everyone together chatting about it. That can be difficult given that everybody has so much work to do, but I think that is the nature of the beast. All we can do is work on ways to communicate better. I have started using Slack as a tool to learn what other people are doing and to communicate with researchers. There has been a lot of emails connecting one another, and you really get a sense that we are all helping one another at this point. 

It is just one of many tools. There are a number of laboratory tools that are proving to be important in this outbreak, including molecular-based diagnostic tools and genomics to understand the spread. We expect that understanding people’s antibody responses is going to be important as well—that is the serology that you might hear people talking about. These are all different laboratory tools that will be really important, and one of the things that continues to be important is how quickly these tests are being developed and deployed. For this outbreak and for future outbreaks, development and deployment of tests are really important factors in preparedness.   


Will We See Another Pandemic Like This? What Must We Invest in Now to Be Ready for It?  

I do not know if we will see a pandemic this big again, but there will be other emergent diseases. This will not be the last time that a new disease emerges, and so one of our priorities is making sure that we have the ability to scale up a response just like this time. I think that we witnessed a rapid and aggressive response, and that is a testament to the science and data available to support those decisions. Continued investment in public health and research will be important in making sure that we have that rapid response in the future.  

A lot of the innovation we are seeing is because of past investments, and we need to make sure those investments continue.

None of this can be done without funding. To be prepared for future pandemics we need to invest in public health, scientific technologies and research in general. A lot of the innovation we are seeing is because of past investments, and we need to make sure those investments continue so that we have a strong public health function and strong research community.  

Investing in academic research is really important as well. Continued research on basic science and applied sciences, public health and training programs is really important. One of the key tools for us is genomics, but there is not a genomics-specific training program—either on the laboratory side of the informatics side. I think continued investment in informatics and modelling will be very important.  


What Has Covid-19 Revealed About Canada’s Dependency on International Sources of Essential Medical Goods and Technologies?  

One of the things we have learned from this outbreak is that we are very dependent on technology companies outside of Canada. For example, with the global demand for testing supplies, we are in competition with other nations. One of the drivers behind our testing challenges is the accessibility of testing kits. I think we need to build the Canadian economy so that the health sector can rely on continuous suppliers. That will be very important in the future. 

I do think we are seeing a number of Canadian companies repurposing some of their production for things like personal protective equipment and we may see materials for diagnostic tests available in the future.  


What is Ignored in Media Coverage of the Crisis That Canadians Should know About?  

A lot of attention has been placed on testing numbers and how many people have been tested. But nobody has been talking about the method to test or what we are doing with the data. We should be thinking about where we are in terms of automation, testing technologies and genomic technologies. We have come a long way, and had this outbreak occurred ten years ago—or even five years ago—we would not be in the place that we are today. We should be focusing on the technology side of things, how grateful we should be for how far we have progressed over time, and the investments that need to continue in order to improve the technology yields in this country. 


As an Infectious Diseases Expert, What Is a Contrarian View You Have on Diseases Such as COVID-19 or Our Response to Them?  

Today we were chatting about the fact that hard respiratory illness diagnoses are down right now. Likewise, the rates of diarrheal disease are down as well—and that is not for lack of submissions, it is because we believe that social distancing and increased hygiene are contributing to a decrease in the spread of infectious diseases. We actually saw this during H1N1 as well. When that outbreak of influenza occurred, we saw less diarrheal infections because of changes in isolation, cleaning procedures and hand hygiene because people were worried about contracting the disease.  

I have been washing my doorknobs, my kids sing Happy Birthday twice and they wash their hands many times a day more than they ever did before. As a society, if we move toward some of these better hygiene practices, we might see a reduction in the burden of infectious diseases. There should not be a silver lining in any of this, but I do think that better knowledge of hygiene can only be a good thing for society. 


How Are Our Canadian Researchers Faring Personally Through This Crisis?  

This is probably one of the most stressful times of my life. But we are in public health for a reason, and we are there for this type of scenario—that is what really motivates us. There is a lot of pressure, but that is our job, and this is what people working in public health and research are built for. We are happy to rise to the cause. That is not to say that there have not been many sleepless nights, but it is our responsibility.  

We are in public health for a reason, and we are there for this type of scenario—that is what really motivates us. 


How Are You Managing Life in the Crisis?  

I have two young children at home, and it has been nice to go to them, have cuddles and have time together. That adds so much fulfilment to my life and it is such a stress reliever to have a dance party with a two-year-old and a five-year-old. That is a way that I destress—just being silly with them. Going on walks around the neighbourhood and taking time to be with family is really important.