Researchers at the British Columbia Centre for Disease Control (BCCDC) are using genomic sequencing to figure out where new cases of coronavirus in the province are coming from and to monitor any spread within the community.
A grant of $150,000 provided by Genome BC’s Strategic Initiatives Fund has allowed the team to begin their work at the same time that B.C. reported its first positive case of coronavirus last month.
“We were able to get funding from Genome BC very quickly,” said Dr. Natalie Prystajecky, a microbiologist overseeing the COVID-19 test development at the BCCDC, in a phone call with Victoria Buzz.
“We put forward the proposal once we knew about the virus but before we had any cases in B.C. The funding came through the same week when we had our first positive case in the end of January or early February.”
Process and application
Identifying the sequence of DNA (or related RNA) for each new strain of the virus in each new patient allows researchers to place that strain in the larger family tree.
This kind of characterization then informs real time decision making, allowing the BC CDC to work with public health authorities to guide and evaluate interventions.
The new project, called “Responding to Emerging Serious Pathogen Outbreaks using Next-gen Data: RESPOND”, is developing a rapid response pilot that will be able to produce sequence and family tree information using palm-sized, mobile controlled tools.
According to Dr. Prystajecky, the first sequence of the novel coronavirus was published in China on January 10th. The technology itself has been used for the past decade, but this new project attempts to refine the technique and make the process faster.
“Once we’ve developed the method, the hope is that we can use it as a tool to help us understand this virus in B.C.,” said Dr. Prystajecky.
“Primarily we can use it to understand virus transmission. As cases become positive we’d sequence the virus and see if it’s spreading in the community.”
The technology can also be used to figure out how the virus is changing or evolving in the host, and information from genome sequencing could help doctors understand which drug treatments would be most effective.
Further, Dr. Prystajecky adds that developing the techniques and tools to respond quickly to viruses can also be applied to other viruses or pathogens of concern, including norovirus and Hepatitis C.
Genome sequencing of this particular novel coronavirus is currently being conducted around the world, and B.C. is leading the research in Canada.
“With SARS, it took the world six months to obtain one virus sequence and B.C. was first,” says Dr. Richard Harrigan, a scientist with decades of experience performing translational HIV studies based on genomics.
“With COVID-19, we are aiming to turn around sequences from each patient in under 24 hours.”
Besides Dr. Harrigan and Dr. Prystajecky, the research team is also led by BCCDC Public Health Laboratory Medical Director Dr. Mel Krajden, who is one of the investigators from the first team in the world to produce the complete sequence of the SARS virus genome.
Vancouver was chosen as the prime location to conduct this pilot study for various reasons, including its well established public health lab and strong CDC team. On February 24th, the BCCDC was officially authorized for COVID-19 testing by the National Microbiology Lab in Winnipeg.
B.C. and Ontario were also the two provinces projected to have the most number of coronavirus cases, based on SARS results—a projection that has come true as B.C. has had seven diagnosed COVID-19 cases thus far while Ontario reported six.
Another factor was the ability to receive fast funding from Genome BC.
“With this outbreak there’s very open quick communication with frontline users of the data with health authorities, hospitals etc. There’s also precedent with genome sequencing to release data quickly, particularly in an emergency of this calibre, so that data would be made publicly available very quickly,” says Dr. Prystajecky.
This project has a six month term and the first genomics will be sequenced in the upcoming weeks.
In a statement on February 25th, the provincial Ministry of Health addressed the growing number of coronavirus cases around the world and stated that authorities are preparing for the possibility of a pandemic.
As of the time of publication, there are a total of 84,187 cases of coronavirus worldwide, 2,876 deaths, and 36,907 people who have recovered from the illness.