Canadian Association for Clinical Microbiology and Infectious Diseases

Canadian National COVID-19 Genomics Surveillance Priorities for Existing and Emerging Variants of Concern

On behalf of the Genome Canada Canadian COVID-19 Genomics Network (CanCOGeN) and the Canadian Public Health Laboratory Network CanCOGeN Working Group:

The Canadian COVID-19 Genomics Network (CanCOGeN) is performing genomic surveillance of circulating SARS-CoV-2 in Canada to track its spread, monitor for variants of concern (VOCs) that might impact transmissibility or disease severity, assist in outbreak investigations, and assess the impact of public health interventions. Recent reports of emerging VOCs with enhanced transmissibility have been reported in the UK and South Africa. The potential for rapid spread of these variants affirms the need for ongoing and enhanced genomic surveillance in Canada and worldwide. Here we set out the national priorities for genomic surveillance, including targeted surveillance of these emerging VOCs.

Priorities for targeted surveillance through whole genome SARS-COV-2 sequencing include:

  1. International travellers.  These include from the United States, and close contacts, from September 1, 2020 until further notice.
  2. Suspected reinfection. Defined reinfection as clinical recurrence of symptoms compatible with COVID-19, accompanied by positive PCR (Ct<35), more than 90 days after the onset of the primary infection.
  3. Severe acute COVID-19 in individuals <50 years old without significant comorbidity. 
  4. Vaccinated individuals with subsequent laboratory-confirmed SARS-CoV-2 infection.
  5. Known or suspected superspreading events. Defined as an outbreak where there is additional epidemiological and/or genomic evidence of one person with overdispersed transmission of COVID-19, (i.e., directly transmitting to at least five non-household individuals).

Specimens identified from these targeted populations should be be forwarded to CanCOGeN partner labs for priority genome sequencing and analysis. Partner laboratories include provincial public health, healthcare and academic laboratories; please connect with your sequencing partner laboratory in anticipation.

The full CanCOGeN National Surveillance Priorities document can be found here: CanCOGen VOC Surveillance