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PHO Rounds: SARS-CoV-2 Genomics for Public Health Surveillance

Since March 2020, Public Health Ontario and the Ontario Covid-19 Genomics Network have sequenced over 27,000 SARS-CoV-2 genomes in support of the pandemic response. From initial characterization of a novel pathogen to identifying the emergence of Variants of Concern, this presentation will describe the evolution of SARS-CoV-2 genomics in Ontario with a focus on applied concepts for public health units. 

Topics covered will include: an overview of SARS-CoV-2 sequencing concepts, general descriptions of testing algorithms and specimen flows, individual result reporting to public health units and the Ontario Laboratory Information System, aggregate surveillance reporting through the SARS-CoV-2 Whole Genome Sequencing in Ontario report, sequencing for outbreak support, and future directions for the genomics program.

By the end of this session, participants will be able to:

  1. Describe the key steps in the process for whole genome sequencing of SARS-CoV-2 in Ontario
  2. Discuss the role of whole genome sequencing for supporting the pandemic response
  3. Describe the relationship between mutations and lineages for SARS-CoV-2 variants of concern/interest
  4. Locate and identify key components of PHO genomics program outputs to support surveillance efforts

Présentateur(s): Alex Marchand-Austin and Dr. Samir Patel

Alex Marchand-Austin is the Genomics Program Lead at Public Health Ontario and completed his MSc at the University of Toronto in the Laboratory Medicine and Pathobiology program, focusing on whole genome sequencing of Bordetella pertussis. Prior to returning to PHO in 2021, Alex held various roles with the Public Health Agency of Canada and Public Health Ontario related to laboratory-based surveillance of infectious diseases.

Dr. Samir Patel
is a Deputy Chief of Microbiology and Laboratory Science at PHO. Dr. Patel has been with PHO since 2009 and has been the clinical lead of many programs at the laboratory, including antimicrobial resistance, tick –borne pathogens including Lyme disease, and has been the lead of the PHO laboratory scientific program since 2017. During the pandemic, Dr. Patel has been involved in the many aspects of COVID, most notably as scientific lead for PHO’s COVID-19 genomics program. He is also an associate professor in the Department of Laboratory Medicine and Pathobiology at the University of Toronto.


Public Health Ontario Rounds are a self-approved group learning activity (Section 1) as defined by the Maintenance of Certification Program of the Royal College of Physicians and Surgeons of Canada (RCPSC). In order to receive written documentation for Continuing Medical Education (CME) credits, please check “Yes” beside the question “Do you require CME credits?” on the registration form.

College of Family Physicians of Canada (CFPC) Affiliate Members may count RCPSC credits toward their Mainpro+ credit requirements. All other CFPC members may claim up to 50 Certified credits per cycle for participation in RCPSC MOC Section 1 accredited activities.

PHO Rounds are also approved by the Council of Professional Experience for professional development hours (PDHs) for members of the Canadian Institute of Public Health Inspectors (CIPHI).

For more information or for a record of registration for other Continuing Education purposes, please contact capacitybuilding@oahpp.ca .


Public Health Ontario is committed to complying with the Accessibility for Ontarians with Disabilities Act (AODA). If you require accommodations to participate in this event, please contact 647-260-7100 or capacitybuilding@oahpp.ca .

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Mis à jour le 2 nov. 2021