title: Molecular characterization of rotavirus isolates from select Canadian pediatric hospitals.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: National Microbiology Laboratory, Winnipeg, Canada.
authors.forename: Andrew
authors.initials: A
authors.lastname: McDermid
authors.forename: Nicole
authors.initials: N
authors.lastname: Le Saux
authors.forename: Elsie
authors.initials: E
authors.lastname: Grudeski
authors.forename: Julie A
authors.initials: JA
authors.lastname: Bettinger
authors.forename: Kathy
authors.initials: K
authors.lastname: Manguiat
authors.forename: Scott A
authors.initials: SA
authors.lastname: Halperin
authors.forename: Lily
authors.initials: L
authors.lastname: Macdonald
authors.forename: Pierre
authors.initials: P
authors.lastname: Déry
authors.forename: Joanne
authors.initials: J
authors.lastname: Embree
authors.forename: Wendy
authors.initials: W
authors.lastname: Vaudry
authors.forename: Timothy F
authors.initials: TF
authors.lastname: Booth
mesh_terms: D000293:Adolescent; D000956:Antigens, Viral / Q000235:genetics; D002170:Canada / Q000453:epidemiology; D036022:Capsid Proteins / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D005243:Feces / Q000821:virology; D005260:Female; D005759:Gastroenteritis / Q000453:epidemiology / Q000821:virology*; D005838:Genotype; D006776:Hospitals, Pediatric; D006801:Humans; D007223:Infant; D008297:Male; D017720:Molecular Epidemiology; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012401:Rotavirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012400:Rotavirus Infections / Q000453:epidemiology / Q000821:virology*
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; C060339:VP4 protein, Rotavirus; C050779:VP7 protein, Rotavirus