A team of researchers across the country is well on their way to learning more about the genetic composition of the virus responsible for COVID-19. In April, Genome Canada announced a $40 million federally funded genomics project that would aim to understand both the SARS-CoV-2 virus and the genomes of infected patients.
The project involves two parts: the first, sequencing the entire genomes of up to 10,000 patients infected with the virus (termed the host genome project). The second is being led by DMCBH researcher Dr. Terry Snutch (pictured) with the goal of sequencing up to 150,000 viral genomes isolated from infected people.
For the host project, patients will be sampled for their genomes, as well as for virus samples, and will also undergo blood testing for virus levels and immune biomarkers. The idea is to create a biobank—a large collection of biological samples—in order to track changes throughout the course of infection and recovery.
The genome sequencing aspect of the project, which is being led by Dr. Snutch, will focus specifically on the virus’ genome. Currently, DNA sequencing is used to diagnose a person with COVID-19. A sample is collected through a nasal or throat swab, and DNA is sequenced using PCR analysis for the presence of VIRUS-specific sequences. The test looks for a small region of the virus’ genome, whereas the full genome sequencing that Dr. Snutch and the Canadian COVID-19 Genome virus project team (called CanCOGeN-VirusSeq) are undertaking will test samples to determine the entire virus genome from thousands of infected patients.
To establish CanCOGeN-VirusSeq, Dr. Snutch coordinated all 13 provincial and territorial health labs, the National Microbiology Lab in Winnipeg, genome sequencing centres, universities and research institutes across the country, as well as 40 hospitals who are all working together to better understand the virus. Sequencing will happen in many labs across the country, including at Dr. Snutch’s lab in UBC’s Michael Smith Laboratories.
“I am very pleased that in the span of about six weeks, all parties came on board and have enthusiastically focused their expertise and resources towards contributing to the viral genome project,” says Dr. Snutch. “Thanks to this quick collaborative start, we’ve already generated about 2,500 viral genomes from across Canada, and I expect that the output will increase substantially as the various sites ramp up their in-house sequencing capabilities.”
The goal of sequencing the virus’ genome is threefold: the first, is to be able to “watch” the virus as it mutates and accumulates changes in the genome. This can be used to track in near real time where a particular variant arose in both time and place, which in turn tells health authorities whether that particular strain of the virus came into a community via external travel or if was already there and is now being spread within a community. The second, is to identify any mutations that pop up which might affect ongoing vaccine efforts or make the virus drug resistant. The third, is to detect any mutations that could impact how efficiently the virus can spread and infect people.
“Our genome sequencing work with the BC-CDC has already shown that some of the earliest virus introductions into B.C.—from the Princess cruise ship, China and Iran—no longer exist in B.C. as actively propagating virus strains,” says Dr. Snutch.
Dr. Snutch’s lab has historically focused on studying the roles of ion channels in brain disorders and has also spent the last seven years doing extensive development of a 3rd-generation sequencing platform now being employed across CanCOGeN-VirusSeq.
“While the last four months have been very intensive and time consuming, it has been energizing to interact with a broad spectrum of highly talented scientists singly focused on making meaningful contributions to Canadians during the pandemic,” says Dr. Snutch.
This article was part of a series originally published on the Djavid Mowafaghian Centre for Brain Health website which focused on Covid-19 work.