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Genotyping COVID-19

This is a guest post from former Genome Alberta staffer Adam Kirkby. You can contact him by email anytime.  
 
It should come as no surprise that many researchers are passionate about the benefits and positive effects of genotyping in humans. With a simple saliva sample an individual can find out a wealth of information about themselves, including family history, susceptibility to diseases, overall health, and which medications they will respond best too. But there is nothing to say that this technology is limited to Homo Sapiens, after all every living creature uses genetic material as the fundamental basis for life and if we can discover so much about ourselves, we can apply the technology to other organisms and find out just as much.
 
This certainly seems to be the thinking of Dr. Mathew Croxen’s group who were recently funded under the CIHR Novel Coronavirus Rapid Research funding program with additional funding from Alberta Innovates. The project aims to pioneer a reliable way of genotyping COVID-19 that is both rapid and affordable for frontline use in the fight against COVID. Like the information generated from genotyping a person, genotyping a virus can be hugely insightful into both where the virus came from and what its future prospects are.
 
According to Dr. Croxen, by tracking the different strains and lineage of the virus we can make accurate predictions on how the virus is spreading, how effective potential vaccines or treatments might be, and how quickly it is changing. All these details will be massively beneficial for guiding public health policy. But the work could also help inform us about COVID-19’s origins and how it made the jump from animal to human in the first place. Similar to how whales have adapted to life in the ocean, even though their skeletons and lungs suggest that their ancestors came from the land, the novel coronavirus genetic code suggests previous strains were far more at home in either pangolins or bats before making the jump to humans.
 
Considering genotyping humans is quite well established you would be forgiven for wondering why genotyping COVID-19 is such a challenge. Well, viruses are a little bit different from most life as we understand it. For starters they aren’t technically alive by our current definitions, and exist in a sort of grey area. But the crux of the problem lies in the fact that viruses do not have DNA, they instead rely on single stranded RNA to replicate which is far more unstable and prone to degradation.

Humans also produce and use RNA, but since DNA is more stable, all our current technology is designed to sequence DNA. So the viral RNA must be converted into DNA before being analysed in a manner that only sequences viral RNA, without including any of the naturally occurring human RNA in a sample.
 
It’s quite the challenge, but if Dr. Croxen and his colleagues across Canada can streamline this process, it will give us new insights into COVID19 and how it is affecting Canadians to help with not only this pandemic but also future viral outbreaks.

Genotyping COVID-19

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