August 2021: Updates to COVID-19 Variants and Laboratory Testing

8 Sep 2021

Important note: Starting November 12, 2021, we have made further updates to our Variants of Concern laboratory testing. Check out our COVID-19 laboratory testing and whole genome sequencing webpages to learn more.

As new and emerging variants become known, laboratory systems around the world, including our lab at Public Health Ontario (PHO) — which is part of the provincial laboratory network — are required to adapt and shift to proactively monitor for these variants and understand how they are spreading in Ontario.

Starting August 2021, PHO has made updates to part of its laboratory testing strategy for COVID-19 – particularly the provincial whole genome sequencing strategy (WGS). Below, we outline changes to our laboratory testing strategy and provide a refresher on how PHO tests for COVID-19 variants of concern (VOC) and what updates we have made to our laboratory testing strategy.

What’s new with PHO’s COVID-19 lab testing for variants?

There have been no changes to the COVID-19 diagnostic and VOC test. What’s new is that we have made updates to our COVID-19 whole genome sequencing strategy – shifting our focus to building a robust  surveillance strategy and public reports 

As of August 27, 2021, the provincial COVID-19 whole genome sequencing strategy includes:
  • Half (1 in 2) of all eligible positive COVID-19 samples (from the VOC PCR test) are sent for whole genome sequencing as part of our surveillance strategy. This strategy will continue to detect new and emerging variants, including the Delta variant, in a timely way.
  • This strategy also includes samples from targeted COVID-19 cases such as from the airport, outbreaks in certain situations, suspected vaccine failure or re-infection cases, or requests from the coroner are also sent for sequencing. This will help detect signs of possible emerging variants and identify issues such as outbreaks, travel-related cases or unusual events.

This strategy is based on the increasing rates of COVID-19 in the province combined with capacity of our whole genome sequencing labs. If COVID-19 cases increase beyond our WGS capacity, PHO will adjust its testing strategy.  Taking a random subset of all eligible positive COVID-19 samples ensures that we have enough information to monitor and detect new variants. Targeted surveillance of the groups listed above will also continue.   

Updates to Laboratory Testing - Explained

Whole genome sequencing (WGS) is a significant tool that helps us understand the evolution and spread of the SARS-CoV-2 virus and can inform outbreak control policies and best-practices.

This laboratory process provides an accurate genetic profile or DNA fingerprint, that can detect VOC and VOI, and help understand the relatedness between cases.

What is the process for WGS?

The process involves 4 steps:

  1. A positive viral sample is treated with chemicals to release the genetic material (also known as DNA and RNA), which is then purified.
  2. Scientists make copies of multiple overlapping regions of the genome, an organism’s complete set of DNA, using PCR.  The copies are referred to as a “DNA library”.
  3. The DNA library is loaded into a machine, called a sequencer that allows us to look closer into the DNA structure of the virus.  The result is referred to as “DNA read”.
  4. The sequencer produces millions of DNA reads and through specialized computer programs they are put together in order.  When the process is complete, the genome sequence is ready for further analysis.

Why did we make this change?

Moving to a representative genome sequencing surveillance strategy is aligned with best practices and is also implemented by the European Centre for Disease Prevention and Control and the United Kingdom. This shift allows us to make best use of our resources to monitor and better understand the burden of current VOC in Ontario. It also allows us to identify and track future VOC and VOI in a reliable, timely way.

Refresher: Testing for VOC and VOI at PHO

What types of SARS-CoV-2 variants does PHO look for? What is the difference between a VOI and a VOC?

Viruses change and mutate as part of their normal evolution. When there are many mutations in the genetic code of a virus, this is called a variant.  As with other viruses, variants are common with SARS-Cov-2 (the virus that causes COVID-19). Although many variants will have no difference in the ability to spread or cause more severe disease, some variants have changes (mutations) which may become concerning.

A variant of concern (VOC) is a variant where its changes have a clinical or public health significance that affects one or more of:

  • spread (transmissibility)
  • severity of disease (virulence)
  • vaccine effectiveness
  • diagnostic testing

VOC identified globally and in Ontario include:

  • Alpha (B.1.1.7 variant first identified the UK)
  • Beta (B.1.351 variant first identified in South Africa)
  • Gamma (P1 variant first identified in Brazil)
  • Delta (B.1.617 variant first identified in India)

A variant of interest (VOI) is a variant that may share one or more mutations in common with a VOC, but do not have enough evidence at this time to be considered a VOC.

Current VOI identified globally and in Ontario include:

  • Eta (B.1.525 variant first identified in Nigeria)
  • Iota (B.1.526 variant first identified in the US)
  • Kappa (B.1.617.1 variant first identified in India)
  • Lambda (C.37 variant first identified in Peru)

PHO’s laboratory testing and surveillance strategy includes identifying and monitoring both VOC and VOI.

To learn more about the new naming conventions for VOC and VOI, check out the World Health Organization’s webpage: Tracking SARS-CoV-2 variants.

How does PHO test for COVID-19 and screen for variants? 

PHO’s complete laboratory testing and surveillance strategy includes three key components: 

  • COVID-19 diagnostic testing (through PCR): the test that tells us if someone currently has COVID-19 by looking for even the smallest amounts of the virus’s genetic material. 
  • Whole genome sequencing: a laboratory process that looks (called sequencing) into the structure of a virus by reading its entire genetic code. Sequencing the SARS-CoV-2 virus allows us to learn more about the virus, how it’s spreading and how it’s changing (emerging VOC and VOI). It also allows us to detect any early threats posed by VOI and VOC.
  • COVID-19 VOC testing (through PCR): Eligible samples that tested positive during the initial COVID-19 diagnostic test are currently sent for VOC PCR testing to determine if a mutation indicating VOC is present in the sample. Our test looked specifically for the N501Y and E484K mutations, which are the mutations associated with three of the predominant VOCs: Alpha, Beta and Gamma. Although this approach is fast, it only looks for variants with these specific mutations and may miss the early introduction of new variants of concern.

Why isn’t the Delta included in the COVID-19 VOC PCR test?

The current approach VOC PCR testing was designed for early detection of the Alpha, Beta and Gamma variants, which at the time of creating the test, were considered rare. This approach was then complemented by whole genome sequencing to confirm the specific variant where needed. This approach has given us a good picture of these three variants. 

However, now that VOC are more common, VOC PCR testing is limited in its timeliness of identifying new variants and is particularly important as we monitor for variants that may appear in vaccinated populations. Our new updates to the whole genome sequencing strategy – where a representative sample of COVID-19 samples are sent for whole genome sequencing – allows us to identify and monitor VOC and VOI in a more proactive and timely way.

Where can I find information and data on COVID-19 variants?

PHO has been working closely with partner labs that perform genome sequencing in Ontario to build and streamline the process of gathering information and reporting on VOCs. We have a series of routine reports and tools where you can find more information, including:

  1. Ontario COVID-19 Data Tool: Provides information on COVID-19 activity in Ontario to-date, including VOC daily case counts and rates for the Alpha, Beta and Gamma variants.
  2. COVID-19 in Ontario: Daily and Weekly Epidemiological Summaries: provides daily and weekly data on VOCs, including the number of confirmed COVID-19 cases or VOC detected.
  3. New Epidemiological Summary: SARS-CoV-2 Whole Genome Sequencing: This summary includes data on VOCs (including the Delta variant) and VOIs from our whole genome sequencing activities conducted by PHO and our partner labs in the Ontario COVID-19 Genomics Network.

If you are responsible for laboratory testing, check out our SARS-CoV-2 (COVID-19 Virus) Variant of Concern Surveillance Test Information Sheet and Labstract for more information.

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Updated 8 Sep 2021