A look inside: B.C.'s whole genome sequencing lab on the hunt for Omicron COVID-19 variant

Every positive COVID-19 sample in B.C. is now being sent to the province’s whole genome sequencing lab in Vancouver, where they are being analyzed to determine if the patient was infected with the Omicron variant.

B.C. Centre for Disease Control microbiologist Natalie Prystajecky said the variant "has a characteristic genetic sequence."

"It has over 50 mutations across the entire genome, and even just 30 of the them in the spike alone," she said. "So when we are looking at the data, we are looking specifically for those mutations.”

This week, the unique mutations were detected in the positive test of a person who had recently returned to B.C. from Nigeria. It was B.C.’s first case of the Omicron variant.

The sample had been analyzed using a specialized rapid detection method, which is able to complete whole genome sequencing in about 30 hours, rather than the typical method which takes three to five days.

The rapid result method is being used on positive tests from travellers that had been to impacted regions, and their close contacts.

“It’s very focused on a limited number, but we can get an indication very quickly that this is an Omicron case, which is what we found. And then that’s fed up to people who need to know in public health, so they can take action,” said BCCDC senior scientist John Tyson.

The BCCDC lab can perform whole genome sequencing on 800 samples per day.

“And that exceeds the number of positives in the province so right now, we are going back and sequencing positives from earlier in November, just to make sure we haven’t missed any cases,” said Prystajecky.

So far, only one case has been confirmed to be the Omicron variant in B.C.

“We will need to time to see how quickly it will compete with the current Delta variant that is widespread,” said BCCDC medical director Mel Krajden, adding “We won’t know how effective the current vaccines are against this strain until we have more people infected.”