Pediatric COVID-19 severity by SARS-CoV-2 lineage and vaccine status in Canada: an IMPACT study

Daniel S Farrar; Julie A Bettinger; Aaron J Campigotto; Shelley L Deeks; Olivier Drouin; Joanne E Embree; Elie Haddad; Scott A Halperin; Tajdin Jadavji; Kescha Kazmi; Melanie King; Charlotte Moore Hepburn; Jesse Papenburg; Rupeena Purewal; Manish Sadarangani; Laura Sauvé; Rae S M Yeung; Karina A Top; Fatima Kakkar; Shaun K Morris; Canadian Immunization Monitoring Program, Active (IMPACT) Investigators

doi:10.1038/s41390-025-03853-0

Pediatric COVID-19 severity by SARS-CoV-2 lineage and vaccine status in Canada: an IMPACT study

Pediatr Res. 2025 Jan 24. doi: 10.1038/s41390-025-03853-0. Online ahead of print.

Authors

Daniel S Farrar¹, Julie A Bettinger^{2

3}, Aaron J Campigotto⁴, Shelley L Deeks⁵, Olivier Drouin^{6

7}, Joanne E Embree^{8

9}, Elie Haddad¹⁰, Scott A Halperin¹¹, Tajdin Jadavji¹², Kescha Kazmi¹³, Melanie King¹⁴, Charlotte Moore Hepburn^{15

16}, Jesse Papenburg^{17

18}, Rupeena Purewal^{19

20}, Manish Sadarangani^{2

3}, Laura Sauvé^{2

3}, Rae S M Yeung^{21

22

23}, Karina A Top^#^{11

24}, Fatima Kakkar^#²⁵, Shaun K Morris^#^{26

27

28

29}; Canadian Immunization Monitoring Program, Active (IMPACT) Investigators

Affiliations

¹ Centre for Global Child Health, The Hospital for Sick Children, Toronto, ON, Canada.
² Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada.
³ Division of Infectious Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.
⁴ Division of Microbiology, The Hospital for Sick Children, Toronto, ON, Canada.
⁵ Department of Health and Wellness, Halifax, NS, Canada.
⁶ Division of General Pediatrics, Department of Pediatrics, CHU Sainte-Justine, Montreal, QC, Canada.
⁷ Department of Social and Preventive Medicine, School of Public Health, Université de Montréal, Montreal, QC, Canada.
⁸ Department of Paediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada.
⁹ Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.
¹⁰ Department of Pediatrics and Department of Microbiology, Immunology, and Infectious Diseases, Centre de Recherche Azrieli du CHU Sainte-Justine, Université de Montréal, Montreal, QC, Canada.
¹¹ Canadian Center for Vaccinology, Dalhousie University and IWK Health Centre, Halifax, NS, Canada.
¹² Department of Pediatrics, Alberta Children's Hospital, Calgary, AB, Canada.
¹³ Division of Infectious Diseases, The Hospital for Sick Children, Toronto, ON, Canada.
¹⁴ Canadian Paediatric Surveillance Program, Canadian Paediatric Society, Ottawa, ON, Canada.
¹⁵ Division of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON, Canada.
¹⁶ Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
¹⁷ Division of Pediatric Infectious Diseases, Montreal Children's Hospital, Montreal, QC, Canada.
¹⁸ Division of Microbiology, McGill University Health Centre, Montreal, QC, Canada.
¹⁹ Department of Pediatrics, University of Saskatchewan, Saskatoon, SK, Canada.
²⁰ Division of Paediatric Infectious Diseases, Jim Pattison Children's Hospital, Saskatoon, SK, Canada.
²¹ Division of Rheumatology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada.
²² Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.
²³ Department of Immunology and Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
²⁴ Department of Pediatrics, University of Alberta, Edmonton, AB, Canada.
²⁵ Division of Infectious Diseases, CHU Sainte-Justine, Montreal, QC, Canada. fatima.kakkar@umontreal.ca.
²⁶ Centre for Global Child Health, The Hospital for Sick Children, Toronto, ON, Canada. shaun.morris@sickkids.ca.
²⁷ Division of Infectious Diseases, The Hospital for Sick Children, Toronto, ON, Canada. shaun.morris@sickkids.ca.
²⁸ Department of Pediatrics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada. shaun.morris@sickkids.ca.
²⁹ Clinical Public Health, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada. shaun.morris@sickkids.ca.

^# Contributed equally.

PMID: 39856228
DOI: 10.1038/s41390-025-03853-0

Abstract

Background: Interpretations of pediatric COVID-19 severity are complicated by novel lineages and COVID-19 vaccine introduction. We estimated the risk of severe COVID-19 by SARS-CoV-2 lineage and vaccination status among hospitalized Canadian children.

Methods: Data were collected through the Canadian Paediatric Surveillance Program (April 2020-May 2021) and Canadian Immunization Monitoring Program, ACTive (June 2021-December 2022). Patients <17 years hospitalized for COVID-19 (excluding incidental SARS-CoV-2) at 13 pediatric hospitals were included. Lineages were defined via genetic sequencing or dominant lineage upon hospitalization. Severe disease included intensive care, ventilatory/hemodynamic requirements, systemic complications, and/or death.

Results: We analyzed 3218 COVID-19 hospitalizations, including 81.4% admitted during Omicron predominance. Median age was highest among Delta cases (2.9 years, interquartile range [IQR] 0.2-10.9) and lowest among Omicron BQ.1 cases (0.6 years, IQR 0.2-1.8). Severe COVID-19 remained common in Omicron vs. ancestral cases (27.2% vs. 23.2%). The proportion of hospitalized cases aged 5-16 years declined following the introduction of age-specific COVID-19 vaccines. Vaccination reduced the risk of in-hospital severe disease for ages 12-16 years (two vs. zero doses; adjusted risk ratio 0.49, 95% confidence interval 0.32-0.77).

Conclusion: More children were hospitalized with Omicron lineages than all prior lineages. COVID-19 vaccination was associated with a lower burden of severe disease among ages 5-16 years.

Impact statement: This study estimates the effect of SARS-CoV-2 lineage, Omicron sub-lineage, and vaccination on COVID-19 disease severity, using data from two Canadian national surveillance programs. Few national studies describe the clinical presentation and severity of Omicron sub-lineages among hospitalized children. In Canada, Omicron lineages were associated with substantially more pediatric COVID-19 hospitalizations than all prior lineages combined, though risk of severe COVID-19 was highest during the Delta period. COVID-19 vaccines were associated with reductions in hospitalization (ages 5-16 years) and severe disease (ages 12-16 years) across Omicron sub-lineages.