After the SARS outbreak began unfolding in earnest in 2003, it took about six months for the first genome to be released publicly.
Flash forward nearly two decades later and the genome sequence for the novel coronavirus, or COVID-19, was released in less than two weeks
“That just speaks to how important genomics is and how improved the technologies are to sequence an entire genome of a pathogen,” said Natalie Prystajecky, a microbiologist at the B.C. Centre for Disease Control (BCCDC) who is overseeing COVID-19 test development.
Her organization’s Public Health Laboratory is now putting those technologies to work when tracking COVID-19’s spread through the province.
With funding from Genome BC, the BCCDC is launching a $150,000, six-month pilot study that integrates genomic analysis into its tracking methods.
The goal is to turn around genome sequences from patients within 24-48 hours, which would allow B.C. experts to quickly determine if the strain has a close relative that’s already appeared in the province or if it’s a new introduction already documented in another country or province.
“So it really helps us understand transmission and that can be really important information when investigating a cluster of cases or trying to understand how an organism is spreading throughout the community,” Prystajecky said, adding she expects this method to be deployed in the coming weeks.
“We don’t know what’s going to happen with this outbreak, we don’t know how many cases we’re going to get. And I think it’s important for the labs to be prepared and for Public Health [Laboratory] to be prepared, and this is one of those tools that gives us extra information.”
The initiative, known as RESPOND (Responding to Emerging Serious Pathogen Outbreaks using Next-gen Data), uses specialized sequencing platforms to produce sequence and family tree information.
The sequence device is about the size of a flash drive and can be controlled through mobile technology, according to Prystajecky.
“Genome sequence is not brand new and we use it in our day-to-day lives, for example … to sequence salmonella from humans, animals, food to understand the spread of foodborne pathogens,” she said.
“In terms of applying it to a virus, this is a little bit newer to us. And the technology and the approach we’re using is actually built off of the response to Ebola and Zika virus.”