title: Human group A rotavirus infections in children in Denmark: detection of reassortant G9 strains and zoonotic P[14] strains.
abstract: One of the leading causes of severe childhood gastroenteritis are group A rotaviruses, and they have been found to be associated with ∼40% of the annual gastroenteritis-associated hospitalizations in young Danish children <5years of age (Fischer et al., 2011). In this study, we investigated the diversity of rotavirus strains circulating among young children <5years of age, presenting with gastroenteritis disease either at the general practitioner or in the hospital, during the period 2009-2013. A total of 831 rotavirus positive stool samples were genotyped in the study period, and the majority of samples (74%) were from hospitalized children. G and P genotypes were successfully determined for 826 of samples, with G1P[8] being the most commonly detected genotype. Detection of G1 showed a decreasing trend over time, and an inverse trend was seen for the emerging G9P. The common human genotypes (G1/G3/G4/G9P[8] and G2P[4]) were detected in the majority of samples (n=733, 88.2%). Rare genotype combinations such as G6P[14] were detected in <1% of samples. Rare genotype strains and strains which failed to amplify in genotyping RT-PCR were subjected to genetic characterization by sequencing one or all of the following genes; VP7, VP4, VP6 and NSP4. Sequences of sufficient length and quality were available for all 4 genes for 28 strains. Phylogenetic analysis revealed that reassortant G9P[4] strains circulated with 3 different genotype combinations. As rotavirus vaccines are not widely used in Denmark or its neighboring countries, the diversity of rotavirus strains identified in this study most likely reflects naturally occurring selection pressures and viral evolution.
authors.affiliation: Section for Virus Surveillance and Research, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: S
authors.initials: S
authors.lastname: Midgley
authors.affiliation: Section for Virus Surveillance and Research, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark; Clinical Microbiology, Laboratory Medicine Malmö, Lund University, Malmö, Sweden.
authors.forename: B
authors.initials: B
authors.lastname: Böttiger
authors.affiliation: Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.
authors.forename: T G
authors.initials: TG
authors.lastname: Jensen
authors.affiliation: Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.
authors.forename: A
authors.initials: A
authors.lastname: Friis-Møller
authors.affiliation: Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark.
authors.forename: L K
authors.initials: LK
authors.lastname: Person
authors.affiliation: Department of Clinical Microbiology, Herlev University Hospital, Herlev, Denmark.
authors.forename: L
authors.initials: L
authors.lastname: Nielsen
authors.affiliation: Section for Virus Surveillance and Research, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark.
authors.forename: S
authors.initials: S
authors.lastname: Barzinci
authors.affiliation: Section for Virus Surveillance and Research, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark. Electronic address: thf@ssi.dk.
authors.forename: T K
authors.initials: TK
authors.lastname: Fischer
mesh_terms: D002675:Child, Preschool; D003718:Denmark / Q000453:epidemiology; D005814:Genes, Viral; D005838:Genotype; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D058885:Multilocus Sequence Typing; D011159:Population Surveillance; D015995:Prevalence; D016865:Reassortant Viruses; D012401:Rotavirus / Q000145:classification* / Q000235:genetics*; D012400:Rotavirus Infections / Q000453:epidemiology / Q000821:virology*
keywords: Denmark; Diversity; Genotype; Molecular epidemiology; Rotavirus