COVID-19 Laboratory Testing at Public Health Ontario

Laboratory testing is an essential component of Ontario’s response to COVID-19. Not only because it tells us if someone has COVID-19 or not, but also because it sheds light on where and how the virus is spreading.


What’s new?

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.

As more and more variants appear, the need to proactively identify and detect these variants requires us to shift to a strategy focused on genomic sequencing.

As such we have made updates to our COVID-19 whole genome sequencing (WGS) strategy – shifting our focus from PCR testing to a genomic sequencing strategy will allow us to identify and monitor VOCs, VOIs and other variants in a proactive and systematic way.

As of November 12, 2021, the new provincial COVID-19 genomic sequencing strategy includes:

  • 100% of eligible positive COVID-19 samples are sent for WGS as part of our surveillance strategy. This strategy will continue to detect new and emerging variants, including the Delta variant, in a timely way.
  • The cessation of routine VOC PCR testing of positive COVID-19 samples.
  • The Ontario COVID-19 Genomic Network (OCGN), which includes 5 laboratories in the province including PHO’s, has increased genomic sequencing capacity in the province to approximately 3,500 samples per week, and additional genome sequencing capacity is being built in Ontario as needed.

Laboratory testing is an essential component of Ontario’s response to COVID-19. Not only because it tells us if someone has COVID-19 or not, but also because it sheds light on where and how the virus is spreading.

PHO’s laboratory conducts over 6 million tests every year at our 11 sites across Ontario on a broad range of clinical and environmental samples – operating one of the largest public health laboratory systems in the world.

PHO performs thousands of COVID-19 tests every day in partnership with many hospital, academic and private labs across the province. This network of labs, coordinated by Ontario Health, has come together rapidly since early 2020, in order to meet the increased demand for testing. Find out more about the early days of COVID-19 testing in Ontario.

In addition to performing tests, PHO acts as Ontario’s reference laboratory for COVID-19 testing. This means that we provide support to new labs as they come online with testing and also validate early samples from those labs to confirm the accuracy of the testing. We also validate new test methods (in collaboration with partner labs, including the National Microbiology Lab) and provide expertise to inform the evolution of Ontario’s testing strategy, including how these new methods are implemented.

How is testing for COVID-19 done?

There are two primary methods used in Ontario for COVID-19 testing:

  1. PCR testing (also known as polymerase chain reaction testing), is a type of test that tells us if someone currently has COVID-19. It uses a sample collected with a swab from the person’s nose/throat.

  2. Serology testing tests someone’s blood to see if they have antibodies for COVID-19. This primarily tells us if someone previously had COVID-19. Currently this test is used in limited clinical situations.

Find out more about the difference between these two types of tests and their application.

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.

Who should be tested for COVID-19?

The Ministry of Health develops testing guidance for COVID-19 that is updated as the outbreak continues to evolve and laboratory testing capacity increases.

PHO does not currently recommend routine testing of asymptomatic persons for COVID-19 (outside of those recommended in the guidance from the Ministry of Health, or as directed by the public health unit for public health investigation). However, clinicians should continue to use their discretion to make decisions on which individuals to test.

If you are concerned that you may have been exposed to, or are experiencing symptoms of COVID-19, please visit the Ministry of Health website, take their self-assessment and follow their guidance and instructions. If you are having difficulty breathing or experiencing other severe symptoms, call 911 or go to a hospital emergency room immediately.

Adapting to Future Needs

We work with the Ministry of Health, Ontario Health and other key experts and stakeholders to monitor, provide guidance, and strategize to make sure COVID-19 testing in the province continues to respond to this evolving public health emergency. We explore new test methodologies, like serology, and continue to investigate and validate the use of different types of swabs, reagents, and testing platforms so that our approach can be flexible.

Updated 17 Nov 2021