title: Norovirus diversity in children with gastroenteritis in South Africa from 2009 to 2013: GII.4 variants and recombinant strains predominate.
abstract: From 2009 to 2013 the diversity of noroviruses (NoVs) in children (⩽5 years) hospitalized with gastroenteritis in South Africa was investigated. NoVs were genotyped based on nucleotide sequence analyses of partial RNA-dependent RNA polymerase (RdRp) and capsid genes. Seventeen RdRp genotypes (GI.P2, GI.P3, GI.P6, GI.P7, GI.P not assigned (NA), GI.Pb, GI.Pf, GII.P2, GII.P4, GII.P7, GII.P13, GII.P16, GII.P21, GII.Pc, GII.Pe, GII.Pg, GII.PNA) and 20 capsid genotypes (GI.1, GI.2, GI.3, GI.5, GI.6, GI.7, GI.NA, GII.1, GII.2, GII.3, GII.4, GII.6, GII.7, GII.10, GII.12, GII.13, GII.14, GII.16, GII.17, GII.21) were identified. The combined RdRp/capsid genotype was determined for 275 GII strains. Fifteen confirmed recombinant NoV strains circulated during the study period. NoV GII.P4/GII.4 (47%) and GII.Pe/GII.4 (18%) predominated, followed by GII.PNA/GII.3 (10%) and GII.P21/GII.3 (7%). Other prevalent strains included GII.Pg/GII.12 (6%) and GII.Pg/GII.1 (3%). Two novel recombinants, GII.Pg/GII.2 and GII.Pg/GII.10 were identified. In 2013 the replacement of GII.4 New Orleans 2009 and GII.P21/GII.3, which predominated during the early part of the study, with GII.4 Sydney 2012 and GII.PNA/GII.3 was observed. This study presents the most comprehensive recent data on NoV diversity in Africa.
authors.affiliation: Department of Medical Virology,Faculty of Health Sciences,University of Pretoria,Pretoria,South Africa.
authors.forename: J
authors.identifier: http://orcid.org/0000-0001-6721-1177
authors.initials: J
authors.lastname: Mans
authors.affiliation: Department of Medical Virology,Faculty of Health Sciences,University of Pretoria,Pretoria,South Africa.
authors.forename: T Y
authors.initials: TY
authors.lastname: Murray
authors.affiliation: Virology Division,Centre for Enteric Diseases,National Institute for Communicable Diseases,Sandringham,South Africa.
authors.forename: S
authors.initials: S
authors.lastname: Nadan
authors.affiliation: Virology Division,Centre for Enteric Diseases,National Institute for Communicable Diseases,Sandringham,South Africa.
authors.forename: R
authors.initials: R
authors.lastname: Netshikweta
authors.affiliation: Virology Division,Centre for Enteric Diseases,National Institute for Communicable Diseases,Sandringham,South Africa.
authors.forename: N A
authors.initials: NA
authors.lastname: Page
authors.affiliation: Department of Medical Virology,Faculty of Health Sciences,University of Pretoria,Pretoria,South Africa.
authors.forename: M B
authors.initials: MB
authors.lastname: Taylor
mesh_terms: D017250:Caliciviridae Infections / Q000453:epidemiology / Q000821:virology*; D036022:Capsid Proteins / Q000235:genetics* / Q000378:metabolism; D002675:Child, Preschool; D005260:Female; D005759:Gastroenteritis / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D008969:Molecular Sequence Data; D029322:Norovirus / Q000235:genetics*; D010802:Phylogeny; D015995:Prevalence; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013019:South Africa / Q000453:epidemiology
chemical_list: D036022:Capsid Proteins; D012324:RNA-Dependent RNA Polymerase
keywords: Norovirus diversity; South Africa; Sydney 2012; norovirus recombinants; paediatric