Monitoring COVID-19 Variants of Concern
25 March 2021
It has often been said that the COVID-19 pandemic is a marathon, not a sprint. True to form, this marathon has not been without its challenges, which have required everyone to adapt and embrace innovative solutions along the way.
The latest challenge in this marathon is the emergence of variant strains of SARS-CoV-2, the virus that causes COVID-19. In mid-December, the United Kingdom (UK) reported a new variant. Other variants of concern (VOC) have been identified in South Africa and Brazil. It is likely other variants will be identified over the course of the pandemic.
What is a variant of concern?
A variant is detected through genomics, which is a field of study that monitors changes in a virus’ genetic material. These changes are known as mutations. Mutations are a normal occurrence with coronaviruses; however, not all mutations have public health and clinical implications. A variant becomes a VOC when its changes have a clinical or public health significance that affects the ability of a variant to:
- Spread in comparison to the original strain
- Cause more severe illness
- Respond to current COVID-19 vaccines and medications
- Be detected in current testing methods
Data suggests that the B.1.1.7 variant first identified the UK, the B.1.351 variant first identified in South Africa, and the P.1 variant first identified in Brazil may be more transmissible than the previously circulating strains. It is still not clear whether the B.1.1.7 variant causes more severe illness. Some studies suggests that it may, while other studies suggests it does not. This is actively being investigated. The Public Health Agency of Canada says the vaccines currently available in Canada are expected to be effective against the variants. More research is happening to confirm this.
Canada recorded its first two cases of the B.1.1.7 variant on December 26, 2020, its first case of the B.1.351 variant on January 8, 2021 and the first case of the P.1 variant on February 7, 2021.
What is PHO doing?
TESTING AND SCREENING
PHO, along with the worldwide scientific and laboratory community, has worked collaboratively throughout the pandemic to monitor SARS-CoV-2 and share those findings to further understanding and knowledge. PHO has been actively performing genomic surveillance of the SARS-CoV-2 virus since the beginning of the pandemic. In mid-December, our laboratory conducted genome sequencing of approximately 250 samples each week for the genetic fingerprints of variants of concern. We increased this to over 800 samples per week in March 2021.
On February 3, 2021, PHO led the provincial diagnostic lab network in testing all positive COVID-19 tests in Ontario for mutations found in predominant VOCs (e.g., N501Y). PHO developed the test which is used to identify the mutations. It has been shared with and adopted by other laboratories in Ontario, as well as laboratories in other provinces and countries.
POINT PREVALENCE STUDY
One important trigger for introducing routine testing for VOCs in Ontario emerged as PHO collaborated with other laboratories on a point prevalence study, where a collection of samples were tested from a particular point in time to get a snapshot of how common VOCs are in Ontario. PHO tested positive SARS-CoV-2 samples in Ontario from January 20, 2021 to identify how many were a VOC. The study found:
- 113 of 2,570 samples (4.4%) screened had the N501Y mutation detected, 88 samples have been confirmed by whole genome sequencing (87 were B.1.1.7 and one was B.1.351)
- Prevalence of the N501Y mutation was 1.1% for samples not associated with an outbreak and 13.2% for samples associated with an outbreak (detected among 2.0% of the different outbreaks tested)
- Prevalence was higher in females for samples associated with an outbreak, and similar for males and females for samples not associated with an outbreak
- Prevalence was higher in older age groups (> 60 years old) for samples associated with an outbreak, and similar across age groups for samples not associated with an outbreak
- 2.5% of samples with N501Y were from individuals with recent international travel
Daily reporting of the data since February 3, 2021 shows exponential increases in the VOC since then, with 30% of all samples tested having the N501Y mutation on March 1, 2021 and a seven-day average of 24.6%.
What else is PHO doing related to VOCs?
- Responding to requests from stakeholders, such as the Ministry of Health, public health units and others for help understanding the VOCs and implications for public health
- Reviewing and synthesizing emerging evidence on VOCs – including implications for public health guidance, measures and infection prevention and control (IPAC)
- Data analysis and reporting to characterize the spread of VOCs in Ontario
- Developing other laboratory tools for detection and research
- Reporting results to public health units to enable public health action
- Providing IPAC and epidemiological support to public health units for outbreak management
Monitoring genetic variations will become increasingly important to inform changes in virus spread, laboratory testing methods, and public health measures. PHO has worked with Ontario’s Provincial Diagnostic Network to ramp up capacity for VOC testing to get even faster results. In addition, PHO is leading genomic sequencing efforts through the Ontario COVID-19 Genomics Network to sequence a minimum of 10% of all positive samples to monitor and identify new and emerging variants in Ontario. Provincially, we are working with laboratory and academic partners, such as the ONCoV Genomics Rapid Response Coalition and the Ontario Science Advisory Table. Nationally, we are collaborating with the Canadian Public Health Laboratory Network, the National Microbiology Laboratory, and the Canadian COVID Genomics Network.
What can Ontarians do to protect themselves?
Regardless of the variant involved, the best way to stop transmission and community spread is to follow public health guidelines – that means limiting contacts as much as possible to your household, physical distancing, masking, staying home if you start having symptoms, and regular hand washing. Visit our Prevention and Management of COVID-19 page for more information.