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Alberta researchers genome sequence COVID-19 samples to track strains of virus, monitor spread

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Work is underway in the province to genome sequence positive samples of COVID-19 collected from Albertans.

Reading the viral genome will allow researchers and scientists to determine the origins of the viruses found in Albertans, such as Asia, Europe or the United States, and how the virus is moving across the province.

The data generated will then be shared in a global database that researchers can use to track mutations in the virus and to develop a vaccine.

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“These mutations, they occur on a regular basis and they occur in a particular geographic location and so, when we see that particular strain end up in Alberta, we’ll be able to track it back,” said Gijs van Rooijen, chief scientific officer of Genome Alberta, which is helping to distribute funds for the project.

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Genome Alberta is one of six regional genome centres, along with federal and provincial public health labs, hospitals and academic institutions that is involved with the research, which is being backed by $40 million of federal funding. Similar work is being done around the world and the data is being shared publicly.

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The genome sequencing will take place at labs in the University of Calgary and University of Alberta, according to van Rooijen, and the rough target is to sequence 10,000 samples from the province.

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Dr. Matthew Croxen, an assistant professor at the Division of Diagnostic and Applied Microbiology at the University of Alberta, who is involved with the project, said most organisms, such as humans, have DNA and RNA.

“This particular virus starts off as RNA and what we want to do is convert it to DNA – what we’re used to, that genetic code.

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“And then we read those building blocks of those different components of the genome and we get a representation of what that genetic makeup is,” he said.

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Dr. Francois Bernier, a clinical geneticist and the head of the Department of Medical Genetics at the University of Calgary, is overseeing the research taking place at the university.

“What do these viruses look like in the province? Are they changing? How are they propagating? How are they moving across the population?” he said.

Bernier said that information will be helpful when looking back on decisions that were made but also looking forward.

“You can use it to retrospectively look at how the outbreak occurred and whether our public health measures were implemented at the right now or whether they were effective or not. You can also use it to continue to understand the current outbreak,” he said.

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To sequence a positive COVID-19 sample, a subsample is created then prepped in the lab before it is put on the sequencer, said Dr. Paul Gordon, bioinformatics manager at the Centre for Health Genomics and Informatics.

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He said the sequencing is critical to finding finer levels of detail about the virus.

“Standard epidemiology works wonderfully at getting associations of data that people remember and you can figure out through pieces of technology such as tracing apps.

“But there’s a lot of what we call cryptic transmission so we don’t actually know where somebody caught the virus and the variants in the virus that are propagating through the population,” he said.

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Researchers across the world are racing to develop a vaccine for the coronavirus, and van Rooijen said genome sequencing will help with that.

“If we see changes in the virus, that may affect our ability to have a very effective vaccine.

“I think, fortunately, this particular virus does not mutate as frequently as, for instance, a regular flu virus.

“The chances we will be developing a vaccine that will be ineffective is… small but it is possible. In that sense, we are very fortunate the mutation rate is rather low,” he said.

Researchers say they expect to genome sequence positive samples in Alberta in the next three to six months.

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