How are COVID-19 variants discovered, tested and tracked?
TORONTO -- Variants of the novel coronavirus are continuing to emerge in Canada, having now appeared in all 10 provinces, although there have been none in the territories so far. Each region has its own approach to testing and tracking, but in general, provinces are now making an effort to test for and track these variants of concern.
HOW MANY CASES GET SCREENED FOR VARIANTS?
With at least three variants now present in Canada, many provinces have begun testing most positive COVID-19 cases for the variants.
In Ontario, they’ve been screening all positive cases for the variants as of Feb. 3. Quebec, Northwest Territories, and Yukon are now sending all positive cases for variant screening too.
In Alberta, up to 300 cases are being sent every day for variant screening, which typically comprises all new positive cases in the province.
New Brunswick and British Columbia have been testing all international travellers for the novel coronavirus, with all positive cases sent for variant screening.
HOW ARE VARIANTS DETECTED?
Samples that are flagged positive for COVID-19 are sent to a provincial laboratory to undergo a polymerase chain reaction test, similar to what all labs have been using to detect the novel coronavirus. This initial screening searches for an N501Y gene mutation in the samples, which is the gene that is currently found in all three variants of concern.
If this gene is detected at this point, the sample is sent for genome sequencing — however, variant cases are not published and added to the variant cases tally until the specific variant type can be identified.
WHAT HAPPENS WHEN A VARIANT IS DETECTED AND IS SENT FOR GENOME SEQUENCING?
Genome sequencing acts as a confirmatory platform to not only verify the presence of the N501Y mutation, but to identify which variant type it is. This method of testing is currently being used to identify the B.1.1.7, B.1.351, and P.1 variants; however, provinces have started to use the sequencing method on a small fraction of cases to screen for possible new and emerging variants.
Because genome sequencing is more expensive than the current novel coronavirus test, only five per cent of cases were previously being tested for variants.
WHEN DOES A VARIANT CASE GET ADDED TO THE PUBLISHED TOTAL?
Results from the initial PCR screening are available 24 hours after the sample is received, while the turnaround time for genome sequencing can take anywhere between seven to 14 days for the results to be published on government sites and reports.
Although these cases are added to the total positive COVID-19 case count, there might be weeks between a person contracting a variant and that case being added to the separate variant tally.
First, a person needs to get a COVID-19 test. Then, that positive test is sent to be screened for the variant mutation, and if the mutation is detected, the sample is then sent for genome sequencing to identify the specific type of variant. Only after those results come back does that information get published on government public health sites and reports.
WHAT ABOUT OTHER VARIANTS?
Provinces are also currently sequencing for new and emerging variants.
Public Health Ontario says that on top of sequencing for the current variants of concern, they will be sequencing up to 10 per cent of all positive cases by Feb. 17. The Quebec Ministry of Health and Social Services is currently sequencing 8.5 per cent as of Feb. 11, but has plans to sequence 10 per cent and later 15 per cent of all cases for newer variants.
In British Columbia, a new variant labelled B.1525 was identified on Feb.12 after a positive case was linked to travel in Nigeria. This variant is the first of its kind to be found in Canada.
Keep track of new daily cases of the variants of concern here.