B.C. labs fast-tracking tests to detect new, more infectious COVID-19 mutations

·3 min read

B.C. laboratories are working on fast-tracking how they test for new, more infectious COVID-19 mutations, so that the province's recent success in flattening its pandemic curve is not quickly undone.

The province's seven-day average of new daily cases is hovering around 481 as of Thursday, but when it comes to genetic code a tiny change could be enough to alter a province's pandemic trajectory.

"It could simply be one single change, and you can imagine the difference between the spelling of new versus now. It could be a subtle change, just one letter different," explained Natalie Prystajecky, a microbiologist at the B.C. Centre for Disease Control.

She says data on the U.K. variant suggests that subtle change is enough to make the new strain 50 per cent more transmissible from person to person than the common strain of SARS-CoV-2. If it spreads, it could dramatically increase the growth rate of the pandemic curve in B.C.

Ben Nelms/CBC
Ben Nelms/CBC

So far, there have been only four confirmed cases of a variant of COVID-19 that first emerged in the U.K. and one case of a mutation originating in South Africa.

Provincial Health Officer Dr. Bonnie Henry said last week that the cases have been isolated and that the new strains aren't yet spreading in the community.

In the meantime, laboratories at the BCCDC are ramping up their capacity to identify cases of the new mutations.

Full genome sequencing

Prystajecky, who is the program head for the environmental microbiology program at the CDC, says the routine COVID-19 test collected by swabs or gargle does not detect the new mutation.

"The spike protein, which is where the majority of mutations occur, is not the best place for a diagnostic target for routine testing," Prystajecky explained.

To identify mutations, labs have to create a full genomic sequence of COVID-19 test samples

The first step involves extracting the nucleic acid — which contains DNA and RNA, the virus's genetic code — a process that can take approximately two days. The nucleic acid is then put into one of the CDC's sequencers which can take up to 19 hours to generate the specific order of letters in the genetic code which can then be analyzed.

Ben Nelms/CBC
Ben Nelms/CBC

"So from end to end, we're looking at three to four days to do all samples tested," said Prystajecky. "We have a higher amount of cases in British Columbia than we have sequencing capacity right now, which is why we're trying to ramp up the amount of screening that we can do for variants of concern."

Those strategies include prioritizing samples from returning travelers for sequencing and developing screening assays that can cut down the time it takes to detect mutations to half a day.

Contact tracing 'on steroids,' says researcher

A mathematical biologist at the University of British Columbia says because the U.K. variant is more infectious, detecting cases has to go hand in hand with more stringent contact tracing..

"One way to do it is to kind of put our contact tracing on steroids," said Sally Otto, who works with a group of researchers on modelling the COVID-19 pandemic in B.C.

Currently, if an individual tests positive for COVID-19, public health authorities will reach out to the recent close contacts of the infected person and ask them to isolate and monitor for symptoms.

"What I mean by [on steroids] is we also ask those contacts to identify the individuals that they have been in recent contact with and really make two layers of protection around these new variants."

Expanding tracing efforts to that second layer of contacts could push B.C.'s contact tracing capacity to its limits, but, Otto says, with the curve flattening, now is the time to double down tracing cases of the new, more infectious variants.