Conducting Whole Genome Sequencing at PHO

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 Variants of Interest (VOI), and help understand the relatedness between cases.

VOC PCR testing has been part of routine testing of positive COVID-19 samples since February 2021. The PCR variant test approach was designed to provide targeted, rapid identification of specific variants that were considered rare at the time for individual case management or local public health control.

More than 99% of sequenced samples identified the Delta variant. VOC PCR looks for a small number of changes in the genetic code of the COVID-19 virus. However, these changes may be shared by many variants. To identify new variants, sequencing of the entire genome is needed. WGS identifies the variant including potential new variants in Ontario, which is important to inform public health response.

This shift to performing WGS on 100% of eligible positive COVID-19 samples and the cessation of routine VOC PCR testing for positive COVID-19 samples will allow us to identify and monitor VOCs, VOIs and other variants in a proactive and systematic way.

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 or RNA, 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 makeup 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.

Laboratory Testing Strategy
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.

Why do we update our testing strategy?
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.


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.

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:

World Health Organization label

PANGO lineage*

First discovered in:

Alpha

B.1.1.7

United Kingdom

Beta

B.1.351

South Africa

Gamma

P.1

Brazil

Delta

B.1617.2

India

*Includes all sub-lineages. For a full list of sub-lineages, please refer to our SARS-CoV-2 Whole Genome Sequencing in Ontario report.

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:

World Health Organization label

PANGO lineage*

First discovered in:

Eta

B.1.525

Nigeria

Iota

B.1.526

United States

Kappa

B.1.617.1

India

Lambda

C.37

Peru

*Includes all sub-lineages. For a full list of sub-lineages, please refer to our SARS-CoV-2 Whole Genome Sequencing in Ontario report.

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 makeup 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.

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. WGS enhanced epidemiological summary, which reports on sequenced samples from the OCGN, which includes data on variants of concern, variants of interest, and other variants being seen in the province.
  2. Historical data on VOCs and mutations in daily and weekly epidemiological summaries can be found on the provincial COVID-19 data webpage.

 

Updated 17 Nov 2021