title: Characterization of GII.4 noroviruses circulating among children with acute gastroenteritis in Pune, India: 2005-2013.
abstract: Genogroup II genotype 4 noroviruses (GII.4 NoVs), an important cause of sporadic childhood gastroenteritis worldwide, undergo continuous evolution leading to the periodic emergence of novel variants. The present study was undertaken for surveillance of GII.4 NoVs and identification and characterization of GII.4 variants circulating among children with sporadic gastroenteritis in Pune, India during 2005-2013. Among the 12 GII genotypes detected in the study, GII.4 was predominant. Sequencing and phylogenetic analysis of ORF2 (major capsid protein VP1 gene) of the GII.4 NoVs revealed circulation of seven GII.4 variants, Hunter_2004 (2005-2007), Yerseke_2006a (2006), DenHaag_2006b (2007), Osaka_2007 (2007-2009), Apeldoorn_2007 (2008), New Orleans_2009 (2008-2012) and Sydney_2012 (2013), with the Pune strains grouping with the contemporary global reference strains. The Hunter_2004, Osaka_2007 and New Orleans_2009 variants showed prolonged circulation, with the Hunter_2004 and New Orleans_2009 variants differentiating into temporally separated sub-clusters. Analysis of VP1 sequences and predicted structures of the GII.4 variants identified variant specific amino acid positions, particularly in and near (within 8A(°)) the epitopes A-E, displaying differences in the sequence and physicochemical characteristics of the different variants. Comparison with the reference strains of each of the GII.4 variants revealed up to 11 amino acid substitutions at the variant specific positions in the GII.4 strains from Pune. Amino acid variations were also noted among the strains of the same GII.4 variant in Pune. The strains of different sub-clusters identified in the Hunter_2004 and New Orleans_2009 variants showed differences in sequence and physicochemical properties of either or all of the epitopes A, C and E. The study thus describes the temporal variations and diversity of the GII.4 strains in Pune and emphasizes continuous monitoring and analysis of the GII.4 variants.
authors.affiliation: Enteric Viruses Group, National Institute of Virology, Pune, India.
authors.forename: Ruta
authors.initials: R
authors.lastname: Kulkarni
authors.affiliation: Enteric Viruses Group, National Institute of Virology, Pune, India.
authors.forename: Amit
authors.initials: A
authors.lastname: Patel
authors.affiliation: Enteric Viruses Group, National Institute of Virology, Pune, India.
authors.forename: Shilpa
authors.initials: S
authors.lastname: Bhalla
authors.affiliation: Enteric Viruses Group, National Institute of Virology, Pune, India.
authors.forename: Preeti
authors.initials: P
authors.lastname: Chhabra
authors.affiliation: Bioinformatics Group, National Institute of Virology, Pune, India.
authors.forename: Sarah
authors.initials: S
authors.lastname: Cherian
authors.affiliation: Enteric Viruses Group, National Institute of Virology, Pune, India. Electronic address: drshobha.niv@gmail.com.
authors.forename: Shobha D
authors.initials: SD
authors.lastname: Chitambar
mesh_terms: D019943:Amino Acid Substitution; D017250:Caliciviridae Infections / Q000821:virology*; D036022:Capsid Proteins / Q000235:genetics*; D002675:Child, Preschool; D005759:Gastroenteritis / Q000821:virology*; D005838:Genotype; D006801:Humans; D007194:India; D007223:Infant; D007231:Infant, Newborn; D029322:Norovirus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny
chemical_list: D036022:Capsid Proteins
keywords: Epitope; GII.4 norovirus; Gastroenteritis; India; VP1; Variant