Open Access Research article

Molecular characterization of rotavirus isolates from select Canadian pediatric hospitals

Andrew McDermid12, Nicole Le Saux3, Elsie Grudeski1, Julie A Bettinger4, Kathy Manguiat1, Scott A Halperin5, Lily MacDonald1, Pierre Déry6, Joanne Embree27, Wendy Vaudry8, Timothy F Booth12* and Members of the Canadian Immunization Monitoring Program, Active (IMPACT)

Author Affiliations

1 National Microbiology Laboratory, Winnipeg, Canada

2 Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada

3 Division of Infectious Diseases, CHEO Research Institute, Children’s Hospital of Eastern Ontario, Ottawa, Canada

4 Vaccine Evaluation Centre, BC Children’s Hospital, University of British Columbia, Vancouver, Canada

5 Canadian Center for Vaccinology, IWK Health Centre and Dalhousie University, Halifax, Canada

6 Centre Mere-Enfant de Quebec, CHUL, and Laval University, Quebec City, Canada

7 Winnipeg Children's Hospital, Winnipeg, Canada

8 Stollery Children’s Hospital and University of Alberta, Edmonton, Canada

For all author emails, please log on.

BMC Infectious Diseases 2012, 12:306  doi:10.1186/1471-2334-12-306

Published: 15 November 2012



We report the first multi-site rotavirus genotype analysis in Canada. Prior to this study, there was a dearth of rotavirus G and P genotyping data in Canada. Publically funded universal rotavirus vaccination in Canada started in 2011 and has been introduced by four provinces to date. Uptake of rotavirus vaccines in Canada prior to 2012 has been very limited. The aim of this study was to describe the genotypes of rotavirus strains circulating in Canada prior to widespread implementation of rotavirus vaccine by genotyping samples collected from selected paediatric hospitals. Secondly we identified rotavirus strains that differed genetically from those included in the vaccines and which could affect vaccine effectiveness.


Stool specimens were collected by opportunity sampling of children with gastroenteritis who presented to emergency departments. Samples were genotyped for G (VP7) genotypes and P (VP4) genotypes by hemi-nested multiplex PCR methods. Phylogenetic analysis was carried out on Canadian G9 strains to investigate their relationship to G9 strains that have circulated in other regions of the world.


348 samples were collected, of which 259 samples were rotavirus positive and genotyped. There were 34 rotavirus antigen immunoassay negative samples genotyped using PCR-based methods. Over the four rotavirus seasons, 174 samples were G1P[8], 45 were G3P[8], 22 were G2P[4], 13 were G9P[8], 3 were G4P[8] and 2 were G9P[4]. Sequence analysis showed that all Canadian G9 isolates are within lineage III.


Although a limited number of samples were obtained from a median of 4 centres during the 4 years of the study, it appears that currently approved rotavirus vaccines are well matched to the rotavirus genotypes identified at these hospitals. Further surveillance to monitor the emergence of rotavirus genotypes in Canada is warranted.