title: Molecular epidemiology of norovirus in Singapore, 2004-2011.
abstract: Norovirus (NoV) is the most common cause of sporadic and epidemic gastroenteritis, globally. This study aimed to investigate the molecular epidemiology of NoV-associated acute gastroenteritis in Singapore by classifying circulating NoV genotypes and genogroup II, genotype 4 (GII.4) variants between September 2004 and February 2011. The temporal dominance and antigenic variation within the circulating epidemic NoV GII.4 variants was also examined, in order to compare the trends in Singapore to those observed globally during the same period. A total of 312 of 1,060 fecal specimens were positive for NoV RNA, using a quantitative RT-PCR. In a subset (125 of 312) of NoV positive samples, the 5' end of ORF2 (region C) of the GI or GII NoV genome was amplified and sequenced. Subsequent phylogenetic analysis identified GII.4 was the most commonly identified genotype representing 80.8% (101/125) of NoV sequenced in this study. The predominant GII.4 variants in circulation during the 2004-2011 epidemic periods were Hunter 2004 (2004-2005), Den Haag 2006b (2006-2009), and New Orleans 2009 (2009-2011). Amino acid variation within the P2 domain of the major capsid protein, VP1, was followed longitudinally within the GII.4 lineage. A constant turnover of variant-specific amino acid change was observed, particularly within the antigenic epitopes A, C and E. In conclusion, this study has characterized the NoV strains in circulation in Singapore between 2004 and 2011. The molecular epidemiology and persistence of GII.4 pandemic NoV lineages in Singapore was similar to trends seen globally, with a noted absence of the Asia 2003 variant.
authors.affiliation: Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
authors.forename: Kun Lee
authors.initials: KL
authors.lastname: Lim
authors.forename: John-Sebastian
authors.initials: JS
authors.lastname: Eden
authors.forename: Lynette L E
authors.initials: LL
authors.lastname: Oon
authors.forename: Peter A
authors.initials: PA
authors.lastname: White
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D019943:Amino Acid Substitution; D000940:Antigenic Variation; D017250:Caliciviridae Infections / Q000453:epidemiology* / Q000821:virology*; D036022:Capsid Proteins / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D016000:Cluster Analysis; D005243:Feces / Q000821:virology; D005260:Female; D005759:Gastroenteritis / Q000453:epidemiology* / Q000821:virology*; D005838:Genotype; D006801:Humans; D007223:Infant; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D029322:Norovirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D016366:Open Reading Frames; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012846:Singapore / Q000453:epidemiology; D055815:Young Adult
chemical_list: D036022:Capsid Proteins; D012367:RNA, Viral
keywords: gastroenteritis; recombination; reverse transcriptase polymerase chain reaction (RT-PCR)