This undated electron microscope image made available by the U.S. National Institutes of Health in February 2020 shows the Novel Coronavirus SARS-CoV-2, yellow, emerging from the surface of cells, blue/pink, cultured in the lab. Also known as 2019-nCoV, the virus causes COVID-19. A medical director at the British Columbia Centre for Disease Control says the numbers of active COVID-19 cases that are variants of concern are higher than what has been publicly reported in the province. THE CANADIAN PRESS/AP-NIAID-RML via AP

This undated electron microscope image made available by the U.S. National Institutes of Health in February 2020 shows the Novel Coronavirus SARS-CoV-2, yellow, emerging from the surface of cells, blue/pink, cultured in the lab. Also known as 2019-nCoV, the virus causes COVID-19. A medical director at the British Columbia Centre for Disease Control says the numbers of active COVID-19 cases that are variants of concern are higher than what has been publicly reported in the province. THE CANADIAN PRESS/AP-NIAID-RML via AP

Variants of concern higher than reported, but giving precise data challenging: BCCDC

VANCOUVER — A medical director at the British Columbia Centre for Disease Control says the number of active COVID-19 cases that are variants of concern is higher than what has been publicly reported in the province.

But Mel Krajden, director of the centre’s public-health laboratory, says providing precise figures for these variant cases is challenging, in part because of the delay to complete whole-genome sequencing and because not all samples can be sequenced.

Data scientists have been calling for more timely, comprehensive information about the variants of concern in B.C. in order to help residents understand the seriousness of the threat and to persuade those who are ignoring public-health orders to follow them.

Provincial health officer Dr. Bonnie Henry said this week that only three per cent of B.C.’s active cases are variants of concern, referring to those that have been confirmed through sequencing. Krajden acknowledged that is “not an accurate representation” of what is happening in the province.

“The numbers are high. Let’s not con ourselves. The numbers are high and they’re not going to get lower. Because this is the same trajectory that we’re following, that Alberta’s following, that Ontario’s following, so we’re not going to get out of this,” he said.

“Either that or you shut down the whole economy, and we’ve been reluctant to be so draconian.”

He said variant of concern cases are doubling about every eight to 10 days and will ultimately replace other COVID-19 strains. But he also said scientists are tracking the variants in a range of ways that go beyond just quantifying them.

“They’re looking at the trends. They’re looking at the people in hospitals. They’re looking at a severity of disease,” he said. “It’s being looked at from many, many different angles, to find: ‘What’s the right solution?’”

Experts have saidthat B.C.’s reliance on time-consuming whole-genome sequencing is not necessary to report cases that are variants of concern. The province already quickly screens about 90 per cent of cases for a mutation that the three major variants have in common.

Ontario reports the number of presumptive variant cases every day based on this quick screening process. It then does whole-genome sequencing on some samples to distinguish between the P.1 variant first identified in Brazil and the B.1.351 variant first found in South Africa.

Henry announced Thursday that B.C. will change how it screens variant of concern cases. Given the growing numbers, the province will assume that presumptive cases identified by the initial screening are the more-transmissible variants, she said, and will treat patients accordingly.

It will use whole-genome sequencing in a more “systematic” way to learn about all the circulating strains, as well as outbreaks and clusters, cases linked to travel and breakaway cases in people who have been immunized, she said.

Henry said the sequencing findings will be reported weekly in BC Centre for Disease Control surveillance reports. But she didn’t say whether the province would report the number of presumptive cases up front, as Ontario does, adding that more would be announced next week.

Krajden said the province stopped trying to sequence all variant of concern cases as of April 1.

“What we wanted to make sure is that we don’t waste our energy on confirming a U.K. variant,” he said, adding that sequencing will still be necessary to distinguish between P.1 and B.1.351.

“What we’re really trying to do is be as clear as possible about what’s circulating, what are the risks, are we able to detect enough variants of interest, can we do the correlations between what happens to someone who has one of these variants.”

Health officials in B.C. have been reluctant to provide the numbers of presumptive variants of concern because some samples could end up being so-called “variants of interest” that have not been shown to be more transmissible, such as the strain first detected in Nigeria.

However, experts say that the current numbers being given only after confirmation by whole-genome sequencing are not accurate either, because B.C. does not have the capacity to sequence every case.

New data provided by the BC Centre for Disease Control gives insight, for the first time, on the number of presumptive variant cases being picked up by quick screening as part of the PCR test from January through March.

In the second week of January, there were two presumptive variant of concern cases. By the first week of February, there were 22, and by the first week of March there were 438. In the final week of March, there were 2,514, or 51 per cent of B.C.’s positive cases.

Cases confirmed through sequencing in the week of March 21 show 1,183 cases, or 21 per cent of B.C.’s positive cases. This same week, Henry told reporters that the portion of cases that were variants of concern was in the “high teens” to “early 20s.”

The centre for disease control notes that there is a weeklong delay for whole-genome sequencing. Krajden said the province has the capacity to sequence about 1,900 cases a week, though the data shows more than 2,000 cases were sequenced the week of Mar. 21.

Whole-genome sequencing for the final week of March has not yet been completed.

Krajden explained that there are other challenges involved in reporting accurate numbers of variant of concern cases.

Different laboratories use different screens as part of their PCR tests, with St. Paul’s Hospital, for example, developing a screen that can distinguish between the three major variants, while others may only pick up the mutation associated with all three.

Another issue is that some samples can’t be sequenced because the amount of viral load isn’t high enough, he added.

He said he understands the public is being “driven crazy” and wants more precise data, and his centre is trying to present the information in as accurate and clear a way as possible.

But he stressed the ultimate goal was immunizing all eligible adults who want the vaccine.

“The endgame is through vaccination, converting a virus that causes severe … disease and death in predominantly the elderly into a virus that causes basically the typical common cold.”

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